Population biobanks: Organizational models and prospects of application in gene geography and personalized medicine

Population biobanks are collections of thoroughly annotated biological material stored for many years. Population biobanks are a valuable resource for both basic science and applied research and are essential for extensive analysis of gene pools. Population biobanks make it possible to carry out fundamental studies of the genetic structure of populations, explore their genetic processes, and reconstruct their genetic history. The importance of biobanks for applied research is no less significant: they are essential for development of personalized medicine and genetic ecological monitoring of populations and are in high demand in forensic science. Establishment of an efficient and representative biobank requires strict observance of the principles of sample selection in populations, protocols of DNA extraction, quality control, and storage and documentation of biological materials. We reviewed regional biobanks and presented the organizational model of population biobank establishment based on the Biobank of Indigenous Population of Northern Eurasia created under supervision of E.V. Balanovska and O.P. Balanovsky. The results obtained using the biobanks in transdisciplinary research and prospective applications for the purposes of genogeography, genomic medicine, and forensic science are presented.     

生物样本库及其伦理问题简介

随着分子和基因组信息对流行病学影响的增加,无数遗传流行病学研究和后人类基因组计划的研究都越来越依赖人类生物样本库的使用。生物样本库的范围也已横跨学术或者医院环境下的小数量收集到大规模的全国性储藏。尽管生物样本库的概念并不新,但是在基因组研究和后人类基因组计划的背景下,伴随它们十几年极大发展的是无数待解决的伦理挑战。从生物样本库的概念着手,介绍了其与一般遗传数据库的区别以及建立生物样本库的意义;然后介绍并比较国际上已有的生物样本库,以及其伦理问题和伦理法律框架的发展趋势。     

Ethical issues and GenomEUtwin.

The post-genomic era is witnessing a proliferation of large-scale and population based genetic and genomic research projects. Many countries have or are establishing research biobanks and, as with GenomEUtwin, there is great interest in building multinational projects that link genotypic and phenotypic information from different centers. Clearly, the conduct of these projects raises multiple ethical issues, and the knowledge generated will continually recast the ethical, legal and social implications (ELSI) of such research. Maximising the scientific profit from this work while minimizing the risks to the participants requires full integration of ethics components into the structure and functioning of these projects. GenomEUtwin is organized around five intellectual cores, including an Ethics Core which operates across the entire project. This paper describes the role of the Ethics Core and presents an overview of the guidelines on which the principles followed in GenomEUtwin are based. We outline the major ethical concerns of our project and highlight complexities arising from diverse national legislations. Finally, the role of empirically based ethics research is discussed for understanding the ethical, legal, social and economic implications of human genetics and genomics research.     

A Proposed Approach to Informed Consent for Biobanks in China

Biobanks are potential goldmines for genomics research. They have become increasingly common as a means to determine the relationship between lifestyle, environmental exposures and predisposition to genetic disease. More and more countries are developing massive national scale biobanks, including Iceland, the UK and Estonia. Now several large‐scale regional and national biobanks are planned in China, such as Shanghai Biobank, which is defined as a key‐element in Shanghai's twelfth five‐year Development Plan of Science and Technology. It is imperative that the authors who are in charge of the ethical aspect of Shanghai Biobank discuss the ethical aspects of these biobanks up front. Currently there is a great deal of heterogeneity in the approaches to informed consent taken by different countries. In the article, after briefly introducing the biobanks in China, we focus on the three most common approaches: classical informed consent, tiered consent, and one‐time general (or blanket) consent, and propose a version of the latter for China, based on compelling arguments.     

Informed consent,and an ethico- legal framework for paediatric observational research and biobanking: the experience of an Italian birth cohort study

Birth cohort studies are important tools for life-course epidemiology, given the spectrum of the environmental, behavioural, and genetic factors that should be considered when making judgements on human health. Biobanks are valuable components of studies designed to investigate the genetic variability of diseases and improve phenotypic characterisation. In studies involving vulnerable populations and biobanks, it is essential to provide ethical reasoning and analyse the legal requirements. We describe the processes and the tools used in the iterative design of an appropriate informed consent model and the ethico-legal framework of the Piccolipiù study. The Piccolipiù study is a prospective population-based study funded by the Italian Ministry of Health that intends to enrol 3,000 newborns and their mothers in five Italian cities, and to store biological samples for future use. To realise these objectives, we performed a thorough evaluation of the literature, of national and international guidelines, and of the impact of the Italian legal requirements for research biobanking. Discussions among stakeholders facilitated the design of the informed consent and the ethico-legal framework. Several topics are addressed, including the suitability of a broad informed consent for paediatric biobanks, infant vulnerability, access to and sharing of data, and the disclosure of individual’s genetic results. Discussion of the ethical and legal procedures adopted in epidemiological biobanking might be a fruitful ground for comparison both at the national level, where standardization and homogeneity are lacking, and at the international level, where different regulatory issues are often in the background and might hamper research biobanks networking.     

Closure of population biobanks and direct-to-consumer genetic testing companies

Genetic research gained new momentum with the completion of the Human Genome Project in 2003. Formerly centered on the investigation of single-gene disorders, genetic research is increasingly targeting common complex diseases and in doing so is studying the whole genome, the environment and its impact on genomic variation. Consequently, biobanking initiatives have emerged around the world as a tool to sustain such progress. Whether they are small scale or longitudinal, public or private, commercial or non-commercial, biobanks should consider the possibility of closure. Interestingly, while raising important ethical issues, this topic has hardly been explored in the literature. Indeed, ethical issues associated with sale, insolvency, end of funding, or transfer of materials to other entities (which are all issues either related to or possible consequences of closure) are seldom the subject of discussion. In an attempt to fill this gap, this paper will discuss—using population and direct-to-consumer (DTC) genetic testing companies’ biobanks as case studies—(1) international and national normative documents addressing the issue of closure and (2) the internal policies of population biobanks and DTC genetic testing companies. The analysis will inform the debate on biobank closure and elucidate the underlying ethical issues, which include, but are not limited to informed consent, storage and privacy.     

Biobanks for genomics and genomics for biobanks

Biobanks include biological samples and attached databases. Human biobanks occur in research, technological development and medical activities. Population genomics is highly dependent on the availability of large biobanks. Ethical issues must be considered: protecting the rights of those people whose samples or data are in biobanks (information, autonomy, confidentiality, protection of private life), assuring the non-commercial use of human body elements and the optimal use of samples and data. They balance other issues, such as protecting the rights of researchers and companies, allowing long-term use of biobanks while detailed information on future uses is not available. At the level of populations, the traditional form of informed consent is challenged. Other dimensions relate to the rights of a group as such, in addition to individual rights. Conditions of return of results and/or benefit to a population need to be defined. With 'large-scale biobanking' a marked trend in genomics, new societal dimensions appear, regarding communication, debate, regulation, societal control and valorization of such large biobanks. Exploring how genomics can help health sector biobanks to become more rationally constituted and exploited is an interesting perspective. For example, evaluating how genomic approaches can help in optimizing haematopoietic stem cell donor registries using new markers and high-throughput techniques to increase immunogenetic variability in such registries is a challenge currently being addressed. Ethical issues in such contexts are important, as not only individual decisions or projects are concerned, but also national policies in the international arena and organization of democratic debate about science, medicine and society.     

Biobanken

Biobanks have become an indispensable component of biomedical research. However, the long-term and unrestricted use of data and biomaterials included in most biobanks pose several legal, ethical and organizational challenges. Therefore, the German Telematics Platform for Medical Research Networks (TMF) has instigated a number of projects addressing the problems arising from the establishment and maintenance of biobanks, each time aiming at the provision of generic solutions to the research community in the form of texts and concepts. After a representative review of existing biobanks in Germany and Europe we provide an overview of the TMF work on biobanking. In addition, two infrastructural projects will be reviewed which should render biobanking in Germany and Europe more efficient and transparent in the future, namely the “Biobanking and Biomolecular Resources Research Infrastructure”(BBMRI) of the European Commission and the National Biobank Register that is currently being set up by the TMF.     

Biobanks: transnational, European and global networks.

Biobanks contain biological samples and associated information that are essential raw materials for advancement of biotechnology, human health, and research and development in life sciences. Population-based and disease-oriented biobanks are major biobank formats to establish the disease relevance of human genes and provide opportunities to elucidate their interaction with environment and lifestyle. The developments in personalized medicine require molecular definition of new disease subentities and biomarkers for identification of relevant patient subgroups for drug development. These emerging demands can only be met if biobanks cooperate at the transnational or even global scale. Establishment of common standards and strategies to cope with the heterogeneous legal and ethical landscape in different countries are seen as major challenges for biobank networks. The Central Research Infrastructure for Molecular Pathology (CRIP), the concept for a pan-European Biobanking and Biomolecular Resources Research Infrastructure (BBMRI), and the Organization for Economic Co-operation and Development (OECD) global Biological Resources Centres network are examples for transnational, European and global biobank networks that are described in this article.     

Issues in pre-implantation genetic diagnosis

Abstract

Whereas in many instances the use of ethnic and religious categories as well as assumptions about the proclaimed homogeneity of populations in the context of biobanks have spurred discussions and public debates in other Western countries, these categories have not been problematized publicly in Israel. This paper argues that this is due to the important function of ethnicity, religious affiliation and family origin in structuring the public sphere. It should be seen in a political context in which the maintenance of clear boundaries between population sub-groups portrays itself as a necessary means for the survival of the Jewish collective. Israeli biobanks, although they do not create new collective identities, serve as important tools to ‘preserve’ the boundaries of existing ones. In this light, biobanks can be seen as repositories for the ‘genetic components’ of the collective body.     

Children and biobanks: a review of the ethical and legal discussion

The use of tissue samples from children is vital to genetic research. Collections of such tissue, in so-called biobanks, can take the form of large-scale prospective cohort studies or disease-specific studies using tissue of children with that specific disease. Collections of samples gathered in a diagnostics context, such as blood spot cards, can also be used for genetic research. Research on stored tissue samples from children poses ethical questions that are different from those posed by the use of samples from adults. Also, the ethical questions raised by the participation of children in biobanks are not analogous to those raised by the participation of children in clinical trials. In this review we first give an overview of the international ethical guidelines and legal regulations concerning biobanking and minors. Next, we review the different themes that occur in the ethical literature on this subject. Specifically we focus on questions of risk and benefit, consent and assent and the return of individual results. We also discuss the concept of solidarity, which is a relatively new concept in the context of children and biomedical research. To conclude, we discuss the gaps and questions raised by the review.     

Eco‐genomic analysis of the poleward range expansion of the wasp spider Argiope bruennichi shows rapid adaptation and genomic admixture

Poleward range expansions are commonly attributed to global change, but could alternatively be driven by rapid evolutionary adaptation. A well‐documented example of a range expansion during the past decades is provided by the European wasp spider Argiope bruennichi. Using ecological niche modeling, thermal tolerance experiments and a genome‐wide analysis of gene expression divergence, we show that invasive populations have adapted to novel climatic conditions in the course of their expansion. Their climatic niche shift is mirrored in an increased cold tolerance and a population‐specific and functionally differentiated gene expression response. We generated an Argiope reference genome sequence and used population genome resequencing to assess genomic changes associated with the new climatic adaptations. We find clear genetic differentiation and a significant admixture with alleles from East Asian populations in the invasive Northern European populations. Population genetic modeling suggests that at least some of these introgressing alleles have contributed to the new adaptations during the expansion. Our results thus confirm the notion that range expansions are not a simple consequence of climate change, but are accompanied by fast genetic changes and adaptations that may be fuelled through admixture between long separated lineages.     

‘It is an entrustment’: Broad consent for genomic research and biobanks in sub‐Saharan Africa

In recent years, there has been an increase in the establishment of biobanks for genetic and genomic studies around the globe. One example of this is the Human Heredity and Health in Africa Initiative (H3Africa), which has established biobanks in the sub‐region to facilitate future indigenous genomic studies. The concept of ‘broad consent’ has been proposed as a mechanism to enable potential research participants in biobanks to give permission for their samples to be used in future research studies. However, questions remain about the acceptability of this model of consent. Drawing on findings from empirical research about the role of trust in decision‐making, we argue that an account of entrustment may be an appropriate way of addressing current challenges of seeking consent for biobank research in Africa. We propose a set of key points to consider that can support the proposed entrustment framework.     

Domesticated Animal Biobanking: Land of Opportunity

In the past decade, biobanking has fuelled great scientific advances in the human medical sector. Well-established domesticated animal biobanks and integrated networks likewise harbour immense potential for great scientific advances with broad societal impacts, which are currently not being fully realised. Political and scientific leaders as well as journals and ethics committees should help to ensure that we are well equipped to meet future demands in livestock production, animal models, and veterinary care of companion animals.In the last decade, human biobanking has emerged as an important driver of scientific activities, and biobanks are indisputably an invaluable resource for all types of research aimed at improving public health. The combination of accessible and well-characterized biological samples of various types linked with a multitude of associated data is driving scientific discoveries at unprecedented speed and making previously unthinkable lines of research a reality [1,2].Unfortunately, biobanking of animal samples is by far less well-established. In March 2015, Nature published an article, titled “Inside the first pig biobank,” describing a newly established biobank of porcine samples to be used in studying human diabetes and hailing it as a pioneering effort in animal biobanking [3]. A PubMed search confirmed that in comparison to human biobanking there appears to be negligible activity in the animal biobanking sector. Searching titles, abstracts, and keywords with the search keys “biobank,” “biobanking,” “genebank,” and “gene bank” and limiting the results to publication dates in 2015, only 9 of 498 search results referred to animal biobanks (see S1 Data). This apparent lack of activity in the animal biobanking sector is also reflected in a 2015 editorial of Biopreservation and Biobanking, the official journal of the International Society for Biological and Environmental Repositories (ISBER), which caters to biobanks of any species. The authors conclude that even though there has been increasing participation from the non-human biobanking sector in the annual ISBER meetings, there is still a pronounced lack of submissions to the journal pertaining to non-human biobanking, and human biobanking issues continue to dominate ISBER activities [4]. The roadmap of the European Council’s European Strategy Forum on Research Infrastructures (ESFRI) reveals that there are projects under way involving human (Biobanking and BioMolecular Resources Research Infrastructure [BBMRI]), marine (European Marine Biological Resource Centre [EMBRC]), microbial (Microbial Resource Research Infrastructure [MIRRI]), and mouse model (Infrafrontier) biobanks, with general animal biobanks starkly missing on that list [5].Naturally, some non-human biobanks storing animal samples, amongst others, do exist. The most active are likely the natural history collections, because they have the intrinsic task to collect, catalogue, and store specimens. The Global Genome Biodiversity Network (GGBN), established in 2011, acts as an umbrella organisation for biodiversity repositories and aims to establish standards and best practices as well as increase sample accessibility through its data portal [6]. A search of the most common domesticated animal species (cattle, sheep, goat, pig, horse, chicken, and dog) yielded only 13 records in the GGBN member repositories.However, some domesticated animal biobanks and less formalized sample collections can be found. Their hosting institutions range from veterinary hospitals, zoos, breeding and diagnostics companies, national farm animal genetic resource gene banks, to research institutes and universities. Depending on their purpose, the stored types of samples vary greatly and range from healthy tissue samples, diseased pathogenic tissue samples, DNA, and RNA to reproductive materials. An example of a well-established physical non-human biobanking infrastructure serving a university is the Swedish University of Agricultural Sciences’ (SLU) Biobank (http://www.slu.se/slubiobank). This biobank also offers a data portal for increasing the visibility and accessibility of non-human sample collections no matter where they are stored. This data portal would be redundant if all samples, together with their associated data, were stored in established biobanks that ensured the visibility of their samples through a network such as GGBN. In contrast, the European Genebank Network for Animal Genetic Resources (EUGENA), coordinated by the European Regional Focal Point on Animal Genetic Resources (http://www.rfp-europe.org), is an emerging networking activity specifically targeting only national farm animal genetic resource collections [7]. These disparate examples demonstrate that there is a lack of a unified and generalized approach to sample collections in the domesticated animal sector.Nonetheless, there are numerous examples of how different disciplines and stakeholders, and ultimately the general public, have already benefitted from the availability of biobanked domesticated animal samples.Even though the pig biobank was commended as a pioneering effort [3], there are in fact a number of biobanks that accommodate animal models for the study of human disease. The domestic dog, for example, with its unique population history, breed structure, and hundreds of spontaneous genetic conditions has proven to be an excellent model for gene mapping in simple and complex disorders [8]. Targeted and effective breeding programs over the past 150 years have created hundreds of distinct breeds that form genetic isolates with reduced genetic heterogeneity. This simplifies genetic studies because fewer susceptibility loci with higher impact contribute to complex disease and allow genetic breakthroughs with smaller study cohorts as compared to the corresponding human conditions [9].The annotation of the canine genome facilitated a rapid evolution of genomic tools and development of several canine biobanks across the continents [10]. Collectively, these biobanks house hundreds of thousands of DNA samples and tissue specimens for hundreds of conditions with medical relevance to humans. Importantly, many canine biobanks maintain active collaborative networks with the breeder community and dog fanciers as well as veterinary clinics and hospitals for patient recruitment and health updates.Besides playing an instrumental role for human health, biobanked animal samples heavily impact developments in food production and the sustainable management of the world’s finite resources. Biobanks in animal breeding, often referred to as gene banks, were initially established with the advent of new reproductive techniques, such as artificial insemination, and typically stored semen and embryos. These biobanks recently played a critical role in the swift implementation of genomic selection, which uses genome-wide SNP markers to predict the genetic merit of breeding individuals [11,12]. The efficient use of genomic selection requires large reference panels of individuals whose genetic values are known with high confidence. In cattle breeding, these are bulls with large numbers of offspring with recorded performance data, such as milk yield. Genomic selection could only be implemented so swiftly and successfully because DNA or semen samples from a large number of bulls were available from cattle breeding company biobanks, and these samples could be linked to performance records of the respective bulls’ offspring. This technology was first adopted by the dairy industry and can potentially result in a 60%–120% increase in the rate of genetic gain. Together with advanced genotyping and reproductive technologies, genomic selection has the potential to increase genetic improvement both in often neglected traits, such as feed efficiency and fertility, and in traits that only recently have become of interest, such as methane output in ruminants or adaptation to climate change [12]. Improvements in these traits are of great interest for ensuring global food security and sustainable management of our limited resources. Without the availability of the gene bank samples, as well as associated performance data records, this transformation would have taken decades, if it had happened at all.Biobanks also play an integral part in worldwide conservation efforts to counteract the well-documented loss of genetic diversity in production animals [13,14]. Slowly, the general perception that these repositories are only to be used in emergencies and as a last resort is changing. In 2012, the USDA National Animal Germplasm Program, for example, harboured more than 700,000 gamete and tissue samples from over 18,000 animals representing more than 130 breeds. From this repository, samples from more than 3,300 animals had been requested and distributed for use in research and industry by 2012. The applications included quantitative trait locus (QTL) studies, assessment of genetic distances, cryobiology research, generation of an experimental research line, reduction of inbreeding, and re-introduction of genotypic combinations lost in current production populations [14]. Samples from rare and endangered breeds are also finding use in research and development of the leading breeding companies. For example, in the Netherlands, a consortium of university and dairy industry partners genotyped samples from rare local cattle breeds to gain insight into the genetic background of milk fatty acid composition. Genomic-assisted introgression could ultimately be used to introduce favourable alleles found in the rare breeds into more widely used breeds.Biobanked samples also played an important role in fighting a viral infection, infectious pancreatic necrosis (IPN), which is common in farmed fish. This virus can lead to rates of >90% mortality in farmed Atlantic salmon, which, therefore, poses a threat to animal welfare and aquaculture industries. In 2008, a major QTL for IPN-resistance was detected in Atlantic salmon. Already, a year later, AquaGen, which supplies about 55% of Atlantic salmon eggs used commercially in Norway, was employing marker-assisted selection to produce IPN-resistant fish. This swift implementation of the QTL in marker-assisted selection was only possible due to the availability of biobanked samples collected in a challenge test in 2005 [15].In addition to combatting disease in animals, biobanked domestic animal samples also play a crucial role in fighting emerging infectious diseases that are often zoonotic, meaning that they can be transmitted between vertebrate animals and humans. Having access to samples of species that act as reservoirs of a disease greatly facilitates the work of public health responders during infectious disease outbreaks [16]. In this context, the collection and traceable link of associated samples, such as parasites, pathogens, and other microbiota, to their parent sample becomes especially important.We are convinced that these examples leave no doubt that biobanked animal samples hold great potential both for advancing human and animal health and welfare as well as securing future food production. Furthermore, the recent advent of cost-efficient gene modification technologies [17] envisages many production, performance, and health applications in livestock and companion animals and further adds interest in animal biobanks.When examining the causes for the low levels of activity in large-scale domesticated animal biobanking, both in regard to the establishment or use of existing physical biobanking infrastructures as well as overarching data portals, a number of hypotheses come to mind. The industries connected to domesticated animal biobanking, such as livestock and companion animal production and veterinary care, are dwarfed by the healthcare industry, so monetary incentives would presumably play a much smaller role. Legislation may have acted as a driver in the formalization and shaping of biobanks and differential legislation regarding the handling, storage, and sharing of human versus animal biosamples, and associated data may thus have led to disparate developments. It is moreover conceivable that the community around domesticated animal biobanking is more fragmented and consists of more diverse stakeholders (academic, non-profit, industrial) than the human biobanking community, which could explain the absence of large-scale cooperative umbrella projects. Moreover, there may be greater difficulties in drafting material transfer agreements for reproductive materials than for other types of samples.We will only be able to exploit the full potential if we, in parallel with human and biodiversity biobanking, tackle the challenges of standardized sampling, processing, and storage, sample visibility and accessibility, standardized codes for diagnoses, collection and storage of associated data with the possibility for updates, as well as ethical and regulatory issues. Here, it is advisable that the domesticated animal sector ensures full compatibility with and relies on existing initiatives wherever feasible. Especially important in this context is to ensure a link between samples and associated phenomic and genomic data, such as derived sequence data. To achieve agreement on standards, both in terms of sample processing and storage and sample visibility and accessibility, actors from veterinary hospitals, zoos, breeding and diagnostics companies, national farm animal genetic resource gene banks, research institutes, universities, and policymakers need to join forces. This is where we momentarily see a lack of coordinated efforts.To respond to these challenges and to ensure that we are well equipped to meet future demands in livestock production, animal models, and veterinary care of companion animals, we propose that scientific and political leaders need to (i) acknowledge the inadequacy of the current situation, (ii) create opportunity and support for the establishment of an international research infrastructure for animal biobanking, and (iii) motivate academic and industrial stakeholders to develop and coordinate biobanks based on lessons learned from human and biodiversity biobanking.In Europe, the European Council’s ESFRI could play a leading role in the establishment of a domesticated animal biobanking network, including best practices, direly needed standards, and a common ontology. In a landscape analysis of European research infrastructures, the 2016 ESFRI roadmap acknowledges a gap in the agricultural and bio-economy sector and explicitly lists livestock facilities including gene banks [5]. While an increase in activities regarding biobanking of farm animal genetic resources is certainly relevant, we consider this not to be far-reaching enough. A step in the right direction would be to begin with compiling information on all existing animal biobanks, analogous to BBMRI’s catalogue for European human biobanks [18], which currently contains information on 340 biobanks (http://www.bbmriportal.eu/).Moreover, ethics committees should require the storage of samples and associated data in formalized biobanks for the approval of scientific experiments. Similarly, journals should apply the same standard to samples and associated data, as they currently apply to molecular data, in terms of storage in formalized repositories prior to publication.     

Biobanks and the phantom public

This paper surveys the current state of knowledge about the relationship between different national publics and biobanks, how different publics perceive biobanks, and which issues are identified as important by various stakeholders. We discuss existing studies and emerging governance strategies dealing with the biobank–publics interface and argue that the search for phantom (biobank) public(s) is on, but still much needs to be done. We argue that the existing data originate in a relatively few regions, among them Northern Europe, the United Kingdom, and in certain U.S. states and are often based on survey research with small samples and short questionnaires. Combined usage of qualitative and quantitative methodology in studies is still rare though of great importance in order to investigate distributions of public opinion and also to be able to explain these patterns. Many important questions in the relationship between publics and biobanks are unexplored, or the existing data are inconsistent.     

Across language families: Genome diversity mirrors linguistic variation within Europe

Objectives: The notion that patterns of linguistic and biological variation may cast light on each other and on population histories dates back to Darwin's times; yet, turning this intuition into a proper research program has met with serious methodological difficulties, especially affecting language comparisons. This article takes advantage of two new tools of comparative linguistics: a refined list of Indo‐European cognate words, and a novel method of language comparison estimating linguistic diversity from a universal inventory of grammatical polymorphisms, and hence enabling comparison even across different families. We corroborated the method and used it to compare patterns of linguistic and genomic variation in Europe. Materials and Methods: Two sets of linguistic distances, lexical and syntactic, were inferred from these data and compared with measures of geographic and genomic distance through a series of matrix correlation tests. Linguistic and genomic trees were also estimated and compared. A method (Treemix) was used to infer migration episodes after the main population splits. Results: We observed significant correlations between genomic and linguistic diversity, the latter inferred from data on both Indo‐European and non‐Indo‐European languages. Contrary to previous observations, on the European scale, language proved a better predictor of genomic differences than geography. Inferred episodes of genetic admixture following the main population splits found convincing correlates also in the linguistic realm. Discussion: These results pave the ground for previously unfeasible cross‐disciplinary analyses at the worldwide scale, encompassing populations of distant language families. Am J Phys Anthropol 157:630–640, 2015. © 2015 Wiley Periodicals, Inc.     

Recent trends in breeding populations of some common trans-Saharan migrant birds in northern Europe

Population trends of some common trans-Saharan migrant birds, mostly passerines, were investigated using data from breeding census schemes in five northern European countries during the periods 1976-89 and 1981-89. Overall, census data for the 14 species censused in all five countries show about equal numbers of increases and decreases. This is not as expected from the work of Berthold et al. (1986) for birds breeding and on migration in central Europe. Comparison of results between national schemes shows no evidence for overall differences in trends. Correlations in census results between the different schemes, species by species, were mainly positive. For all five countries, there were more positive than negative correlations between year-to-year population changes and an appropriate measure of African rainfall.     

The impact of population structure on genomic prediction in stratified populations

Key message

Impacts of population structure on the evaluation of genomic heritability and prediction were investigated and quantified using high-density markers in diverse panels in rice and maize.

Abstract

Population structure is an important factor affecting estimation of genomic heritability and assessment of genomic prediction in stratified populations. In this study, our first objective was to assess effects of population structure on estimations of genomic heritability using the diversity panels in rice and maize. Results indicate population structure explained 33 and 7.5 % of genomic heritability for rice and maize, respectively, depending on traits, with the remaining heritability explained by within-subpopulation variation. Estimates of within-subpopulation heritability were higher than that derived from quantitative trait loci identified in genome-wide association studies, suggesting 65 % improvement in genetic gains. The second objective was to evaluate effects of population structure on genomic prediction using cross-validation experiments. When population structure exists in both training and validation sets, correcting for population structure led to a significant decrease in accuracy with genomic prediction. In contrast, when prediction was limited to a specific subpopulation, population structure showed little effect on accuracy and within-subpopulation genetic variance dominated predictions. Finally, effects of genomic heritability on genomic prediction were investigated. Accuracies with genomic prediction increased with genomic heritability in both training and validation sets, with the former showing a slightly greater impact. In summary, our results suggest that the population structure contribution to genomic prediction varies based on prediction strategies, and is also affected by the genetic architectures of traits and populations. In practical breeding, these conclusions may be helpful to better understand and utilize the different genetic resources in genomic prediction.     

Quality matters: International standards for biobanking

Human biospecimens provide the basis for research, leading to a better understanding of human disease biology and discovery of new treatments that are tailored to individual patients with cancer or other common complex diseases. The collection, processing, preservation, storage and providing access to these resources are key activities of biobanks. Biobanks must ensure proper quality of samples and data, ethical and legal compliance as well as transparent and efficient access procedures. The standards for biobanking outlined herein are intended to be implemented in biobanks and to supply researchers with high‐quality samples fitted for an intended use.

Several variables in the pre‐analytical phase can affect the quality of biological samples. © K. Zatloukal.     

Sampling related individuals within ponds biases estimates of population structure in a pond‐breeding amphibian

Effective conservation and management of pond‐breeding amphibians depends on the accurate estimation of population structure, demographic parameters, and the influence of landscape features on breeding‐site connectivity. Population‐level studies of pond‐breeding amphibians typically sample larval life stages because they are easily captured and can be sampled nondestructively. These studies often identify high levels of relatedness between individuals from the same pond, which can be exacerbated by sampling the larval stage. Yet, the effect of these related individuals on population genetic studies using genomic data is not yet fully understood. Here, we assess the effect of within‐pond relatedness on population and landscape genetic analyses by focusing on the barred tiger salamanders (Ambystoma mavortium) from the Nebraska Sandhills. Utilizing genome‐wide SNPs generated using a double‐digest RADseq approach, we conducted standard population and landscape genetic analyses using datasets with and without siblings. We found that reduced sample sizes influenced parameter estimates more than the inclusion of siblings, but that within‐pond relatedness led to the inference of spurious population structure when analyses depended on allele frequencies. Our landscape genetic analyses also supported different models across datasets depending on the spatial resolution analyzed. We recommend that future studies not only test for relatedness among larval samples but also remove siblings before conducting population or landscape genetic analyses. We also recommend alternative sampling strategies to reduce sampling siblings before sequencing takes place. Biases introduced by unknowingly including siblings can have significant implications for population and landscape genetic analyses, and in turn, for species conservation strategies and outcomes.