The Promise and Practicality of Population Genomics Research with Endangered Species

Recent technological advances have dramatically reduced the cost of DNA sequencing. In addition, these methods require lower DNA quantities and qualities than did the previous generation of molecular techniques. As a result, genomic-scale studies of natural populations of endangered species, including those using noninvasively collected samples, are increasingly feasible. Such studies have the potential to advance our understanding of behavior, demography, evolutionary ecology, biogeography, and population history, and to contribute to the prioritization of conservation efforts. I point to a number of salient examples. However, there are also some current limitations and challenges associated with this scale of population genomics research in nonhuman, nonmodel species. Here, I describe the practicalities of the present state of this research while providing what is intended to be a straightforward walkthrough of the technology and methods involved.     

Genetic epidemiological studies of eastern Adriatic Island isolates, Croatia: objective and strategies

In this paper, the authors discuss why isolate island populations represent a particularly helpful model for genetic epidemiological studies. A thorough previous anthropological research carried out in Eastern Adriatic island isolates, Croatia, in terms of ethnohistory, geography and current demography is reviewed. The major results of the studies of population genetic structure of those populations, including model-bound and model-free approaches, the analyses of serogenetic polymorphisms and most recent studies using HLA class II, VNTR and STR DNA polymorphisms, are briefly presented. The organization of health care on the islands is analyzed and some relevant details of specific medical problems and some autochtonous diseases in these island populations is noted. The authors present in outline four illustrative examples of research opportunities which are afforded by the unique circumstances found in these isolate communities. These relate to hereditary dwarfism on Krk island, Mal de Meleda on Mljet island, extreme inbreeding on Susak island and population genetics of cancer on the islands of Brac, Hvar, Korcula, Vis and Lastovo. Finally, the authors develop objectives and strategies for a long-term genetic epidemiological research of these populations and suggest that such a programme of investigation would further our understanding of the causes of (rare) diseases which are uniquely important to these communities but also of common diseases which are important contributors to the burden of disease both in these islands and throughout the world.     

用双单倍体群体构建水稻的分子连锁图

本研究以窄叶青８号（籼稻）×京系１７（粳稻）的Ｆ１花培株系──ＤＨ群体为基础建立了１个水稻的ＲＦＬＰ连锁框架图,该图含ＲＦＬＰ标记、同功酶标记等共１０８个位点,标记间的平均间距为８．６ｃＭ。该图谱与已发表的用其他群体构建的图谱有很高的可比性。利用该框架图定位了２个未知位点的同功酶标记基因和１个籼稻亲本的抗稻瘟病基因。研究表明,目前的群体可进一步扩大成为一个永久性的作图群体,并应用于水稻基因定位和基因组研究     

Toward a new synthesis: population genetics and evolutionary developmental biology

Despite the recent synthesis of developmental genetics and evolutionary biology, current theories of adaptation are still strictly phenomenological and do not yet consider the implications of how phenotypes are constructed from genotypes. Given the ubiquity of regulatory genetic pathways in developmental processes, we contend that study of the population genetics of these pathways should become a major research program. We discuss the role divergence in regulatory developmental genetic pathways may play in speciation, focusing on our theoretical and computational investigations. We also discuss the population genetics of molecular co-option, arguing that mutations of large effect are not needed for co-option. We offer a prospectus for future research, arguing for a new synthesis of the population genetics of development.     

The environment of ageing.

The issue of housing and the wider environment for an ageing population is one where there are many unanswered questions. In this paper a number of key issues are discussed and for each of these the focus is on three aspects. These are the current situation, its reasonableness and what research is needed in order to make decisions about policy and practice. The first three issues relate to the profile of older people themselves and the importance of home to them. The changing profile of older people is not just about an ageing population but also about the growing prominence of those with dementia, women, people from black and ethnic minority groups and one person households, yet little is known about the type of housing which should be provided. Of equal concern is the widening gap between those with a high standard of living (including housing) and those with a low standard of living. The importance of home to older people means that research must focus on how people can be enabled to remain there, and also on the costs, financial and otherwise, to carers and to society. The next three issues relate to the type of housing older people live in and moves in later life. The startling change in the tenure pattern with a growth of owner occupation brings problems as does the decline in social housing. The advantages and disadvantages of the different types of housing--mainstream and specialized--for older people are relatively well known. However the balance between the two needs more research as does that on retirement communities. While it is well known that there are peaks of migration in old age and that moves are often made in haste, little is known about the process of decision making. The final two topics concern links between housing and other aspects of older people''s lives. On health more research is needed on temperature, mortality and morbidity, homelessness and accidents and especially on links between services. These topics have implications for planning and design. The emphasis should be on a multidisciplinary approach using a variety of quantitative and qualitative techniques with an emphasis on dissemination.     

The genetic effective and adult census size of an Australian population of tiger prawns (Penaeus esculentus)

This study compares estimates of the census size of the spawning population with genetic estimates of effective current and long-term population size for an abundant and commercially important marine invertebrate, the brown tiger prawn (Penaeus esculentus). Our aim was to focus on the relationship between genetic effective and census size that may provide a source of information for viability analyses of naturally occurring populations. Samples were taken in 2001, 2002 and 2003 from a population on the east coast of Australia and temporal allelic variation was measured at eight polymorphic microsatellite loci. Moments-based and maximum-likelihood estimates of current genetic effective population size ranged from 797 to 1304. The mean long-term genetic effective population size was 9968. Although small for a large population, the effective population size estimates were above the threshold where genetic diversity is lost at neutral alleles through drift or inbreeding. Simulation studies correctly predicted that under these experimental conditions the genetic estimates would have non-infinite upper confidence limits and revealed they might be overestimates of the true size. We also show that estimates of mortality and variance in family size may be derived from data on average fecundity, current genetic effective and census spawning population size, assuming effective population size is equivalent to the number of breeders. This work confirms that it is feasible to obtain accurate estimates of current genetic effective population size for abundant Type III species using existing genetic marker technology.     

Simulations of the effect of advective-diffusive processes on observations of plankton abundance and population rates

The transport of plankters by water currents is acknowledgedto have an important influence on observations of organism abundanceand population processes, but assessment of this effect hasbeen difficult to achieve. This paper presents simulations usingthe theory of A.Okubo and co-workers. The transport of multiplecurrent drogues over time in a physically realistic advectiveand diffusive current field was simulated. The impact of transportprocesses on the plankton abundance associated with each currentdrogue was then evaluated, and the results are presented graphically.Although plankton numbers were held constant in the simulation,the inferred, but incorrect, population rate parameters thatwould be obtained using successive observations of planktonabundance in the simulated flow field are also presented.     

A practical approach for minimising inbreeding and maximising genetic gain in dairy cattle

A method that predicts the genetic composition and inbreeding (F) of the future dairy cow population using information on the current cow population, semen use and progeny test bulls is described. This is combined with information on genetic merit of bulls to compare bull selection methods that minimise F and maximise breeding value for profit (called APR in Australia). The genetic composition of the future cow population of Australian Holstein-Friesian (HF) and Jersey up to 6 years into the future was predicted. F in Australian HF and Jersey breeds is likely to increase by about 0.002 and 0.003 per year between 2002 and 2008, respectively. A comparison of bull selection methods showed that a method that selects the best bull from all available bulls for each current or future cow, based on its calf''s APR minus F depression, is better than bull selection methods based on APR alone, APR adjusted for mean F of prospective progeny after random mating and mean APR adjusted for the relationship between the selected bulls. This method reduced F of prospective progeny by about a third to a half compared to the other methods when bulls are mated to current and future cows that will be available 5 to 6 years from now. The method also reduced the relationship between the bulls selected to nearly the same extent as the method that is aimed at maximising genetic gain adjusted for the relationship between bulls. The method achieves this because cows with different pedigree exist in the population and the method selects relatively unrelated bulls to mate to these different cows. Selecting the best bull for each current or future cow so that the calf''s genetic merit minus F depression is maximised can slow the rate of increase in F in the population.     

Unbiased relatedness estimation in structured populations

Knowledge of the genetic relatedness between individuals is important in many research areas in quantitative genetics, conservation genetics, forensics, evolution, and ecology. In the absence of pedigree records, relatedness can be estimated from genetic marker data using a number of estimators. These estimators, however, make the critical assumption of a large random mating population without genetic structures. The assumption is frequently violated in the real world where geographic/social structures or nonrandom mating usually lead to genetic structures. In this study, I investigated two approaches to the estimation of relatedness between a pair of individuals from a subpopulation due to recent common ancestors (i.e., relatedness is defined and measured with the current focal subpopulation as reference). The indirect approach uses the allele frequencies of the entire population with and without accounting for the population structure, and the direct approach uses the allele frequencies of the current focal subpopulation. I found by simulations that currently widely applied relatedness estimators are upwardly biased under the indirect approach, but can be modified to become unbiased and more accurate by using Wright's F(st) to account for population structures. However, the modified unbiased estimators under the indirect approach are clearly inferior to the unmodified original estimators under the direct approach, even when small samples are used in estimating both allele frequencies and relatedness.     

Worm control in sheep in the future

Endoparasitic infestations cost the livestock industry many millions of pounds each year through losses in productivity and the costs of control measures. Effective control of these endemic ubiquitous diseases is important, particularly given the expanding world population and the expectation of an increasing demand for ruminant products. Currently, these debilitating ruminant infestations can be controlled prophylactically by using chemotherapy, immunomanipulation and/or management of the grazing environment, but most farmers currently rely upon having effective anthelmintics. Unfortunately, studies on the incidence and prevalence of anthelmintic resistance throughout the world suggest that production systems that are wholly reliant upon intensive chemotherapy/prophylaxis are not sustainable. Current research is examining chemical strategies that will provide good worm control and will also enable the conservation of efficacy of our current and any novel anthelmintics. Maintaining an infra- and supra-population of worms in refugia (i.e., unexposed to anthelmintics) is accepted by most veterinary parasitologists as the best means of maintaining the genes for susceptibility within the parasite population. Maintained susceptibility within a parasite population can be achieved in a variety of ways, all of which utilise a targeted treatment approach to some extent. Whole flock targeted treatment can be optimised using faecal egg count monitoring and individuals can have targeted selective treatments administered on the basis of morbidity markers, such as anaemia, production efficiency assessed by liveweight gain or milk production. There is also a growing interest in bioactive forages, which can have both direct anthelmintic effects and/or indirect anthelmintic effects, where the benefit derives from nutritional effects which boost the host immune responses against nematodes. In the future, arguably the most exciting area is that of immunomanipulation, where current advances in genomics and proteomics offer scope for the development of vaccines and genetic or bio-markers associated with infection or effective immunity. We have been able to identify and select genetically resistant animals for many years by using phenotypic markers for endoparasitism, but it is only recently that the first genetic marker for host resistance has become available. Further research is also needed to identify better phenotypic and genotypic markers for resilience, since in some production systems this may be a more desirable trait than resistance. The implementation of an integrated approach to control to develop sustainable control strategies represents a formidable challenge for the sheep industry. This integrated approach will require well-informed veterinarians; advisors and researchers will need to find the tools to support the practitioners, as well as to find ways of delivering them in an affordable way. Although at present these demands may seem both unobtainable and unaffordable, the development of collaborative multidisciplinary research programmes coupled with advancing high throughput technologies offers the prospect of real progress in this area in future.     

Epidemiological tracking and population assignment of the non-clonal bacterium, Burkholderia pseudomallei

Rapid assignment of bacterial pathogens into predefined populations is an important first step for epidemiological tracking. For clonal species, a single allele can theoretically define a population. For non-clonal species such as Burkholderia pseudomallei, however, shared allelic states between distantly related isolates make it more difficult to identify population defining characteristics. Two distinct B. pseudomallei populations have been previously identified using multilocus sequence typing (MLST). These populations correlate with the major foci of endemicity (Australia and Southeast Asia). Here, we use multiple Bayesian approaches to evaluate the compositional robustness of these populations, and provide assignment results for MLST sequence types (STs). Our goal was to provide a reference for assigning STs to an established population without the need for further computational analyses. We also provide allele frequency results for each population to enable estimation of population assignment even when novel STs are discovered. The ability for humans and potentially contaminated goods to move rapidly across the globe complicates the task of identifying the source of an infection or outbreak. Population genetic dynamics of B. pseudomallei are particularly complicated relative to other bacterial pathogens, but the work here provides the ability for broad scale population assignment. As there is currently no independent empirical measure of successful population assignment, we provide comprehensive analytical details of our comparisons to enable the reader to evaluate the robustness of population designations and assignments as they pertain to individual research questions. Finer scale subdivision and verification of current population compositions will likely be possible with genotyping data that more comprehensively samples the genome. The approach used here may be valuable for other non-clonal pathogens that lack simple group-defining genetic characteristics and provides a rapid reference for epidemiologists wishing to track the origin of infection without the need to compile population data and learn population assignment algorithms.     

Online resources for SNP analysis

The major online single nucleotide polymorphism (SNP) databases freely available as research tools for genetic analysis are explained, reviewed, and compared. An outline is given of the search strategies that can be used with the most extensive current SNP databases: National Centre for Biotechnology Information (NCBI) dbSNP and HapMap to help the user secure the most appropriate data for the research needs of clinical genetics and population genetics research. A range of online tools that can be useful in designing SNP genotyping assays are also detailed.     

Dendritic cells and liver fibrosis

Dendritic cells are a relative rare population of specialized antigen presenting cells that are distributed through most lymphoid and non-lymphoid tissues and play a critical role in linking the innate and adaptive arms of the immune system. The liver contains a heterogeneous population of dendritic cells that may contribute to liver inflammation and fibrosis through a number of mechanisms. This review summarizes current knowledge on the development and characterization of liver dendritic cells and their potential impact on liver fibrosis. This article is part of a Special Issue entitled: Fibrosis: Translation of basic research to human disease.     

The biology of non-weedy hemiparasiticOrobanchaceae: Synthesis and perspectives

This paper gives an overview of current research into the biology of hemiparasiticOrobanchaceae, formerly part of theScrophulariaceae. It is based on presentations and discussions that took place during the First International Symposium on non-weedy hemiparasiticOrobanchaceae in April 2004 in Wageningen. Aspects such as taxonomy and evolution, ecophysiology, population and restoration ecology are discussed, thus identifying challenges for future research. Hemiparasites have very different life histories, and the robust molecular phylogeny will now permit testing hypotheses regarding the evolution of these life histories, degree of parasitism and host specialization. In a number of genera, evolution is in full swing, leading to taxonomical complications, but at the same time offering opportunities for phylogeographical research. In ecophysiology, the challenge is to better understand what makes a good host and to investigate further the chemical signals emitted by the host and their use in regulating parasite development. Finally, the results of sowing hemiparasites to speed up the restoration of nutrient-poor grasslands are still very variable, and we need a more thorough understanding of the factors influencing population dynamics, which should also enable us to devise better management plans for threatened hemiparasitic species.     

Setting Guidelines for Electromagnetic Exposures and Research Needs

Current limits for exposures to nonionizing electromagnetic fields (EMF) are set, based on relatively short-term exposures. Long-term exposures to weak EMF are not addressed in the current guidelines. Nevertheless, a large and growing amount of evidence indicates that long-term exposure to weak fields can affect biological systems and might have effects on human health. If they do, the public health issues could be important because of the very large fraction of the population worldwide that is exposed. We also discuss research that needs to be done to clarify questions about the effects of weak fields. In addition to the current short-term exposure guidelines, we propose an approach to how weak field exposure guidelines for long-term exposures might be set, in which the responsibility for limiting exposure is divided between the manufacturer, system operator, and individual being exposed. Bioelectromagnetics. © 2020 Bioelectromagnetics Society     

Slow motion extinction: inbreeding,introgression, and loss in the critically endangered mangrove finch (<Emphasis Type="Italic">Camarhynchus heliobates</Emphasis>)

The critically endangered mangrove finch is now limited to one small population on the west coast of Isabela Island in the Galápagos, but 100 years ago multiple populations were found on the islands of Isabela and Fernandina. By accessing genetic datasets through museum sampling, we are able to put current levels of genetic diversity and hybridization with congenerics into a historical context for enhanced conservation. In this study, we compared neutral genetic diversity of the now extinct Fernandina population to historical and current diversity of the Isabela population using 14 microsatellite markers. We found that current genetic diversity of the last remnant population (~80–100 individuals) is far below levels 100 years ago, with only about half of the allelic diversity retained. Current genetic diversity is close to levels in the Fernandina population that went extinct by the 1970s. Bottleneck analysis did not show a strong signature of recent decline, and instead implies that this species may have consistently had low population sizes with wide fluctuations. Hybridization with congeneric woodpecker finches was found in the modern Isabela population, implying that some individuals within the few remaining breeding pairs are finding mates with woodpecker finches. Within the context of historical low population sizes and wide fluctuations, current conservation efforts may help the mangrove finch face current extinction threats and avoid the fate of the Fernandina population. However, this historically small lineage will likely continue to face challenges associated with small specialist species surrounded by a widely-distributed sister lineage producing viable hybrids.     

污染物环境生态效应评价研究进展

总结了污染物环境生态效应评价的关键环节--生态受体选择、反应终点和评价参数确定等研究现状,分析讨论了这些环节目前存在的问题和今后的研究方向.个体和种群层次上的生态受体研究较为深入,相应的反应终点研究也较为成熟,但群落和系统层次上的生态受体研究较少,相应的反应终点还不能完整的表征其结构与功能发生的变化.应用能够完整反映生态系统功能及结构组织状态的反应终点,以生态系统为受体进行污染物环境生态效应评价是今后的研究方向.基于假设检验的NOEC只是一个实验设计浓度,不能构造置信区间;ECx由不同的数学模型计算的结果差异较大,置信区间随效应值x的降低而增大.研究综合假设检验与数学模型各自优点的评价参数估算方法是污染物环境生态效应评价的重要研究内容.     

Microsatellite and morphometric variation in Drosophila gouveai: the relative importance of historical and current factors in shaping the genetic population structure

Drosophila gouveai is a cactus-breeding species with a naturally fragmented distribution in central-western and southeastern Brazil. In this study, a neutral genetic marker (microsatellite DNA) and a quantitative trait (wing morphology) were used to investigate the population structure of eight populations of D. gouveai . Quantitative analysis was done using a morphometric approach and multivariate analysis of 17 wing parameters. Drosophila gouveai showed a large degree of genetic population differentiation ( F _ST = 0.245). A molecular analysis of variance showed that the population structure was attributable mainly to genetic differences among the population groups, which were correlated with regional groupings. A Bayesian cluster analysis also identified the same regional groupings as contributing to the population structure. Assignment tests revealed that the current gene flow was very restricted. The divergence in wing morphology among populations was also high, and revealed a geographical pattern that conformed to a latitudinal cline. In contrast to current factors such as migration-drift equilibrium, these results indicated that the genetic population structure of D. gouveai was shaped predominantly by historical factors.     

Autism spectrum disorders in adolescence and adulthood: Long-term outcomes and relevant issues for treatment and research

The advances in research and treatment of autism spectrum disorders(ASD) over the past three decades have focused largely on early childhood and school-age years. Although ASD is a lifelong condition, there has been relatively little attention paid to ASD during the adolescent and adulthood periods. As the population of those with ASD continues to rise and age, the need to provide research and treatment for this group has become increasingly evident. This paper reviews the current literature available on symptoms, functioning, and treatment of adolescents and adults with ASD, as well as the unique issues that arise for individuals with ASD after childhood. Adulthood outcomes for ASD are generally poor, even for those with average to above average cognitive ability. Further research and additional clinical resources are needed for this rapidly increasing group.