The computer program STRUCTURE does not reliably identify the main genetic clusters within species: simulations and implications for human population structure

One of the primary goals of population genetics is to succinctly describe genetic relationships among populations, and the computer program STRUCTURE is one of the most frequently used tools for doing so. The mathematical model used by STRUCTURE was designed to sort individuals into Hardy–Weinberg populations, but the program is also frequently used to group individuals from a large number of populations into a small number of clusters that are supposed to represent the main genetic divisions within species. In this study, I used computer simulations to examine how well STRUCTURE accomplishes this latter task. Simulations of populations that had a simple hierarchical history of fragmentation showed that when there were relatively long divergence times within evolutionary lineages, the clusters created by STRUCTURE were frequently not consistent with the evolutionary history of the populations. These difficulties can be attributed to forcing STRUCTURE to place individuals into too few clusters. Simulations also showed that the clusters produced by STRUCTURE can be strongly influenced by variation in sample size. In some circumstances, STRUCTURE simply put all of the individuals from the largest sample in the same cluster. A reanalysis of human population structure suggests that the problems I identified with STRUCTURE in simulations may have obscured relationships among human populations—particularly genetic similarity between Europeans and some African populations.     

The fate and function of glycosphingolipid glucosylceramide

In higher eukaryotes, glucosylceramide is the simplest member and precursor of a fascinating class of membrane lipids, the glycosphingolipids. These lipids display an astounding variation in their carbohydrate head groups, suggesting that glycosphingolipids serve specialized functions in recognition processes. It is now realized that they are organized in signalling domains on the cell surface. They are of vital importance as, in their absence, embryonal development is inhibited at an early stage. Remarkably, individual cells can live without glycolipids, perhaps because their survival does not depend on glycosphingolipid-mediated signalling mechanisms. Still, these cells suffer from defects in intracellular membrane transport. Various membrane proteins do not reach their intracellular destination, and, indeed, some intracellular organelles do not properly differentiate to their mature stage. The fact that glycosphingolipids are required for cellular differentiation suggests that there are human diseases resulting from defects in glycosphingolipid synthesis. In addition, the same cellular differentiation processes may be affected by defects in the degradation of glycosphingolipids. At the cellular level, the pathology of glycosphingolipid storage diseases is not completely understood. Cell biological studies on the intracellular fate and function of glycosphingolipids may open new ways to understand and defeat not only lipid storage diseases, but perhaps other diseases that have not been connected to glycosphingolipids so far.     

The mystery of the mystery of common genetic diseases

Common monogenic genetic diseases, ones that have unexpectedly high frequencies in certain populations, have attracted a great number of conflicting evolutionary explanations. This paper will attempt to explain the mystery of why two particularly extensively studied common genetic diseases, Tay Sachs disease and cystic fibrosis, remain evolutionary mysteries despite decades of research. I review the most commonly cited evolutionary processes used to explain common genetic diseases: reproductive compensation, random genetic drift (in the context of founder effect), and especially heterozygote advantage. The latter process has drawn a particularly large amount of attention, having so successfully explained the elevated frequency of sickle cell anemia in malaria-endemic areas. However, the empirical evidence for heterozygote advantage in other common genetic diseases is quite weak. I introduce and illustrate the significance of a hierarchy of genetic disease phenomena found within the genetic disease explanations, which include the phenomena: single mutation variants of a common genetic disease, single genetic diseases, and classes of diseases with related phenotypic effects. I demonstrate that some of the confusion over the explanations of common genetic diseases can be traced back to confusions over which phenomena are being explained. I proceed to briefly evaluate the existing evidence for two common human genetic diseases: Tay Sachs disease and cystic fibrosis. The above considerations will ultimately shed light on why these diseases’ evolutionary explanations remain so deeply unresolved after so such a great volume of research.     

HLA and disease.

Many human diseases are associated with HLA class I, class II and class III antigens. It appears that the class III antigen disease associations can be explained by a direct defect operating at the level of either the class III gene or its gene product. The mechanism underlying class I and class II antigen disease associations is at present unknown. In this review we have considered thirty diseases which have been ranked according to their relative risk as defined by the frequency of a given HLA antigen in patient and control populations. The chronic inflammatory disorder, ankylosing spondylitis and its association with HLA B27 has been used as a model to study the HLA linked diseases. We have suggested that the disease may be caused by the Gram-negative microorganism Klebsiella which has antigenic similarity to HLA B27. It is proposed that some antibodies made against Klebsiella bind to HLA B27, thereby acting as autoantibodies leading to the pathological sequelae of chronic inflammatory arthritis. This is the crosstolerance hypothesis or molecular mimicry model and it has been compared to the receptor model. It is further suggested that the crosstolerance hypothesis can be utilised as a general theory to explain the association of other diseases with the class I and class II antigens, and offer a possible explanation for the polymorphism of HLA.     

Ill nature: Disease hotspots as threats to biodiversity

Diseases are part of the natural world, but human activities may affect and disrupt the natural dynamics of diseases, threatening wildlife species and human welfare. We listed the number of species threatened by diseases and compiled their distributional ranges. Based on such data we identify global disease hotspots, regions where disrupted disease dynamics threaten to decimate several species into extinction. The number of species threatened by disease may increase, and climate change may act synergistically increasing the severity of disease incidence in the hotspots, and drive the emergence of new disease hotspots. Until now diseases were thought to play a secondary role in the biodiversity extinction crisis, but the global threat scenario is so dynamic that if we do not bring diseases to the forefront of conservation actions and policies, they may not only bring species into extinction but they may also affect human populations as well.     

Phenotypic variation and selective mortality as major drivers of recruitment variability in fishes

An individual's phenotype will usually influence its probability of survival. However, when evaluating the dynamics of populations, the role of selective mortality is not always clear. Not all mortality is selective, patterns of selective mortality may vary, and it is often unknown how selective mortality compares or interacts with other sources of mortality. As a result, there is seldom a clear expectation for how changes in the phenotypic composition of populations will translate into differences in average survival. We address these issues by evaluating how selective mortality affects recruitment of fish populations. First, we provide a quantitative review of selective mortality. Our results show that most of the mortality during early life is selective, and that variation in phenotypes can have large effects on survival. Next, we describe an analytical framework that accounts for variation in selection, while also describing the amount of selective mortality experienced by different cohorts recruiting to a single population. This framework is based on reconstructing fitness surfaces from phenotypic selection measurements, and can be employed for either single or multiple traits. Finally, we show how this framework can be integrated with models of density‐dependent survival to improve our understanding of recruitment variability and population dynamics.     

Ethics and infectious disease

Bioethics apparently suffers from a misdistribution of research resources analogous to the '10/90' divide in medical research. Though infectious disease should be recognized as a topic of primary importance for bioethics, the general topic of infectious disease has received relatively little attention from the discipline of bioethics in comparison with things like abortion, euthanasia, genetics, cloning, stem cell research, and so on. The fact that the historical and potential future consequences of infectious diseases are almost unrivalled is one reason that the topic of infectious disease warrants more attention from bioethicists. The 'Black Death' eliminated one third of the European population during the 14th Century; the 1989 flu killed between 20 and 100 million people; and, in the 20th Century smallpox killed perhaps three times more people than all the wars of that period. In the contemporary world, epidemics (AIDS, multi-drug resistant turberculosis, and newly emerging infectious diseases such as SARS) continue to have dramatic consequences. A second reason why the topic of infectious disease deserves further attention is that it raises difficult ethical questions of its own. While infected individuals can threaten the health of other individuals and society as a whole, for example, public health care measures such as surveillance, isolation, and quarantine can require the infringement of widely accepted basic human rights and liberties. An important and difficult ethical question asks how to strike a balance between the utilitarian aim of promoting public health, on the one hand, and libertarian aims of protecting privacy and freedom of movement, on the other, in contexts involving diseases that are--to varying degrees--contagious, deadly, or otherwise dangerous. Third, since their burden is most heavily shouldered by the poor (in developing countries), infectious diseases involve issues of justice--which should be a central concern of ethics. I conclude by providing sociological and historical explanations of why the topic of infectious disease has not already received more attention from bioethicists.     

Global stressors and the global decline of amphibians: tipping the stress immunocompetency axis

There is a widespread consensus that the earth is experiencing a mass extinction event and at the forefront are amphibians, the most threatened of all vertebrate taxa. A recent assessment found that nearly one-third (32%, 1,856 species) of the world’s amphibian species are threatened. Amphibians have existed on the earth for over 300 million years, yet in just the last two decades there have been an alarming number of extinctions, nearly 168 species are believed to have gone extinct and at least 2,469 (43%) more have populations that are declining. Infectious diseases have been recognized as one major cause of worldwide amphibian population declines. This could be the result of the appearance of novel pathogens, or it could be that exposure to environmental stressors is increasing the susceptibility of amphibians to opportunistic pathogens. Here I review the potential effects of stressors on disease susceptibility in amphibians and relate this to disease emergence in human and other wildlife populations. I will present a series of case studies that illustrate the role of stress in disease outbreaks that have resulted in amphibian declines. First, I will examine how elevated sea-surface temperatures in the tropical Pacific since the mid-1970s have affected climate over much of the world and could be setting the stage for pathogen-mediated amphibian declines in many regions. Finally, I will discuss how the apparently rapid increase in the prevalence of amphibian limb deformities is linked to the synergistic effects of trematode infection and exposure to chemical contaminants.     

Estrogen receptor concentration and social factors as predictors of natural killer cell activity in early-stage breast cancer patients. Confirmation of a model

Previous work of ours has demonstrated that a significant amount of natural killer (NK) activity variance after surgery in stage I and II breast cancer patients could be accounted for by both the estrogen receptor (ER) status of the tumor and by social factors, namely, perceived social support and seeking social support as a general coping strategy. As considerable evidence has accumulated that social support in both animal and human populations may have survival value, we sought to test the reliability of this regression model, using coping and perceived support factor values obtained at 3 months after surgery to account for concurrent follow-up NK activity in this serially assessed group of patients. It was found that the most significant variable predicting NK activity at follow-up was tumor ER concentration, with higher NK activity associated with ER- status. In addition, seeking social support as a coping strategy, as well as the perceived quality of support, also entered the model to account for a significant amount of NK activity variance (multivariate F = 5.25, p less than 0.001). If, as the literature suggests, NK activity is relevant to breast cancer control, and since ER- tumors have a worse prognosis, we suggest here that perhaps such tumors are resistant to control by NK cells because they lack the ability to attract an accumulation of effector cells to the tumor site, or because blocking factors at the site of the tumor prevent local tumor control at the site of action. The finding related to social support also replicates results from an independent sample of breast cancer patients. This finding, taken together with other evidence that this social variable is associated with longer survival in breast cancer populations, underscores the potential importance of this social support variable. Our findings also suggest one possible immunological variable involved, with potential clinical significance, for this patient population.     

Genetic structure and evolved malaria resistance in Hawaiian honeycreepers

Infectious diseases now threaten wildlife populations worldwide but population recovery following local extinction has rarely been observed. In such a case, do resistant individuals recolonize from a central remnant population, or do they spread from small, perhaps overlooked, populations of resistant individuals? Introduced avian malaria (Plasmodium relictum) has devastated low‐elevation populations of native birds in Hawaii, but at least one species (Hawaii amakihi, Hemignathus virens) that was greatly reduced at elevations below about 1000 m tolerates malaria and has initiated a remarkable and rapid recovery. We assessed mitochondrial and nuclear DNA markers from amakihi and two other Hawaiian honeycreepers, apapane (Himatione sanguinea) and iiwi (Vestiaria coccinea), at nine primary study sites from 2001 to 2003 to determine the source of re‐establishing birds. In addition, we obtained sequences from tissue from amakihi museum study skins (1898 and 1948–49) to assess temporal changes in allele distributions. We found that amakihi in lowland areas are, and have historically been, differentiated from birds at high elevations and had unique alleles retained through time; that is, their genetic signature was not a subset of the genetic variation at higher elevations. We suggest that high disease pressure rapidly selected for resistance to malaria at low elevation, leaving small pockets of resistant birds, and this resistance spread outward from the scattered remnant populations. Low‐elevation amakihi are currently isolated from higher elevations (> 1000 m) where disease emergence and transmission rates appear to vary seasonally and annually. In contrast to results from amakihi, no genetic differentiation between elevations was found in apapane and iiwi, indicating that slight variation in genetic or life‐history attributes can determine disease resistance and population recovery. Determining the conditions that allow for the development of resistance to disease is essential to understanding how species evolve resistance across a landscape of varying disease pressures.     

Climate and New World periosteal reaction patterns: implications for migration routes into the Western Hemisphere

The presence of the diseases yaws and bejel are indicated by periosteal reaction patterns. The distributions of these two diseases in ancient North American human populations show evidence of climatic influence. Those ancient populations lacking either yaws or bejel (the null periosteal reaction pattern) can be found in the coldest parts of the Cold Winter Regions. Those populations with yaws (the poly-ostotic periosteal reaction) can be found in the milder portions of the Cold Winter Regions. The populations with bejel (the pauci-ostotic periosteal reaction) are found either outside of or marginal to Cold Winter Regions. The Bering Strait area is considered to be the gateway to the ancient New World. The cold climates present in this area should have influenced the routes available for the diseases to spread from population to population or by migration of infected populations into the Western Hemisphere. It is suggested that the coastal route with its milder maritime climate was the route taken by yaws when it entered the New World. The presence of bejel in ancient North America presents a conundrum. The climate would have blocked the spread of the disease from Siberia to Alaska in either Late Glacial or Holocene times. This suggests that our present view of migration routes is incomplete.     

Obligatory precautions against infection

If we have a duty not to infect others, how far does it go? This question is often discussed with respect to HIV transmission, but reflection on other diseases like influenza raises a number of interesting theoretical issues. I argue that a duty to avoid infection not only yields requirements for persons who know they carry a disease, but also for persons who know they are at increased risk, and even for those who definitely know they are completely healthy. Given the numerous ways in which human interaction facilitates the spread of communicable diseases, a maximum level of precaution would be very demanding – possibly unreasonably demanding. The ‘over‐demandingness problem’ is mostly invoked as a criticism of utilitarianism, as this theory requires moral agents to always maximise general welfare, even at significant cost for themselves. However, I argue that, with respect to precautions against infectious diseases like influenza, utilitarianism is able to avoid the over‐demandingness problem. A contractualist account, on the other hand, whilst able to explain how one's obligations to avoid infection can be limited, given that other persons have opportunities and responsibilities to protect themselves, in the end requires precautions that raise the over‐demandingness problem.     

Causal Drift,Robust Signaling,and Complex Disease

The phenotype of many regulatory circuits in which mutations can cause complex, polygenic diseases is to some extent robust to DNA mutations that affect circuit components. Here I demonstrate how such mutational robustness can prevent the discovery of genetic disease determinants. To make my case, I use a mathematical model of the insulin signaling pathway implicated in type 2 diabetes, whose signaling output is governed by 15 genetically determined parameters. Using multiple complementary measures of a parameter’s importance for this phenotype, I show that any one disease determinant that is crucial in one genetic background will be virtually irrelevant in other backgrounds. In an evolving population that drifts through the parameter space of this or other robust circuits through DNA mutations, the genetic changes that can cause disease will vary randomly over time. I call this phenomenon causal drift. It means that mutations causing disease in one (human or non-human) population may have no effect in another population, and vice versa. Causal drift casts doubt on our ability to infer the molecular mechanisms of complex diseases from non-human model organisms.     

Genotype and allele frequencies of polymorphic cytochromes P450 CYP1A2 and CYP2E1 in Mexicans

CYP1A2 and CYP2E1 are two of the main cytochrome P450 isoforms involved in the metabolism of commonly used drugs and xenobiotic compounds considered to be responsible for or possible participants in the development of several human diseases. Individual susceptibility to developing these pathologies relies, among other factors, on genetic polymorphism which depends on ethnic differences, as the frequency of mutant genotypes varies in different human populations. Thus the aim of this study was to investigate the frequency of CYP1A2 5'-flanking region and CYP2E1 Rsa I/Pst I polymorphisms in Mexicans by PCR-RFLP methods. The DNA of 159 subjects was analysed and mutant allele frequencies of 30% for CYP2E1 Rsa I/Pst I sites and 43% for CYP1A2 5'-flanking region were found. These frequencies are higher than those previously reported for other human populations.     

Bone marrow transplantation--an expanding approach to treatment of many diseases

Thus, we can conclude that marrow transplantation has already influenced medical practice greatly. It has offered a treatment which often cures patients of more than 20 otherwise lethal diseases. The treatment so horrendously difficult and dangerous at first has already been greatly improved, simplified, and made much safer. The availability of a suitable donor has been much extended and real progress has been made in prevention and perhaps even in treatment of graft-versus-host disease. This has made possible the option of marrow transplantation for every patient in whom we think the treatment may be beneficial. The problem underlying many cases of interstitial pneumonia has been identified and patients are already benefitting clinically from this progress. Progress has also been made which promises antiviral therapy which could reduce, prevent, and ultimately eliminate the intercurrent virus infections which limit the applicability of marrow transplantation, especially for children with severe immunodeficiencies. I do not know how far this line of investigation can be taken. However, just as we have learned stepwise to use marrow transplants from matched siblings to treat many diseases, to use fetal liver in place of bone marrow, to employ matched relative donors when a matched sibling is not available, and, finally, even to use parental donors to achieve correction of SCID, we now have good reason to believe that, ultimately, we can use marrow transplantation without fear of GVHD to address many additional genetically determined and acquired diseases; certainly, for those diseases that involve any of the cells that are derived from bone marrow cells, and perhaps for those attributable even to cells of other organs and tissues, the functions of which are, in whole or in part, a consequence of interactions of marrow-derived cells and cells of ectodermal or endodermal origin, marrow transplantation may be useful. To us, the future of marrow transplantation as a major modality of treatment or prevention of many diseases, including hemoglobinopathesis, immunodeficiencies, hematologic abnormalities, abnormalities of function of marrow-derived cells, and even inborn errors of function of cells of organs and tissues not of marrow origin, seems bright, indeed. Further, with the capacity to introduce resistance genes against viruses and malignancies, autoimmune diseases, and diseases dependent on anomalies of immune response genes, marrow transplantation for many other diseases seems a more remote possibility.(ABSTRACT TRUNCATED AT 400 WORDS)     

HLA class I-associated diseases with a suspected autoimmune etiology: HLA-B27 subtypes as a model system

Although most autoimmune diseases are connected to major histocompatibility complex (MHC) class II alleles, a small number of these disorders exhibit a variable degree of association with selected MHC class I genes, like certain human HLA-A and HLA-B alleles. The basis for these associations, however, has so far remained elusive. An understanding might be obtained by comparing functional, biochemical, and biophysical properties of alleles that are minimally distinct from each other, but are nevertheless differentially associated to a given disease, like the HLA-B*27:05 and HLA-B*27:09 antigens, which differ only by a single amino acid residue (Asp116His) that is deeply buried within the binding groove. We have employed a number of approaches, including X-ray crystallography and isotope-edited infrared spectroscopy, to investigate biophysical characteristics of the two HLA-B27 subtypes complexed with up to ten different peptides. Our findings demonstrate that the binding of these peptides as well as the conformational flexibility of the subtypes is greatly influenced by interactions of the C-terminal peptide residue. In particular, a basic C-terminal peptide residue is favoured by the disease-associated subtype HLA-B*27:05, but not by HLA-B*27:09. This property appears also as the only common denominator of distinct HLA class I alleles, among them HLA-B*27:05, HLA-A*03:01 or HLA-A*11:01, that are associated with diseases suspected to have an autoimmune etiology. We postulate here that the products of these alleles, due to their unusual ability to bind with high affinity to a particular peptide set during positive T cell selection in the thymus, are involved in shaping an abnormal T cell repertoire which predisposes to the acquisition of autoimmune diseases.     

Varying degrees of Apis mellifera ligustica introgression in protected populations of the black honeybee, Apis mellifera mellifera, in northwest Europe

The natural distribution of honeybee subspecies in Europe has been significantly affected by human activities during the last century. Non-native subspecies of honeybees have been introduced and propagated, so that native black honeybee (Apis mellifera mellifera) populations lost their identity by gene-flow or went extinct. After previous studies investigated the remaining gene-pools of native honeybees in France and Spain, we here assess the genetic composition of eight northwest European populations of the black honeybee, using both mitochondrial (restriction fragment length polymorphisms of the intergenic transfer RNAleu-COII region) and nuclear (11 microsatellite loci) markers. Both data sets show that A. m. mellifera populations still exist in Norway, Sweden, Denmark, England, Scotland and Ireland, but that they are threatened by gene flow from commercial honeybees. Both Bayesian admixture analysis of the microsatellite data and DraI-RFLP (restriction fragment length polymorphism) analysis of the intergenic region indicated that gene-flow had hardly occurred in some populations, whereas almost 10% introgression was observed in other populations. The most introgressed population was found on the Danish Island of Laeso, which is the last remaining native Danish population of A. m. mellifera and the only one of the eight investigated populations that is protected by law. We discuss how individual admixture analysis can be used to monitor the restoration of honeybee populations that suffer from unwanted hybridization with non-native subspecies.     

WEIRD bodies: mismatch,medicine and missing diversity

Despite recent rapid advances in medical knowledge that have improved survival, conventional medical science's understanding of human health and disease relies heavily on people of European descent living in contemporary urban industrialized environments. Given that modern conditions in high-income countries differ widely in terms of lifestyle and exposures compared to those experienced by billions of people and all our ancestors over several hundred thousand years, this narrow approach to the human body and health is very limiting. We argue that preventing and treating chronic diseases of aging and other mismatch diseases will require both expanding study design to sample diverse populations and contexts, and fully incorporating evolutionary perspectives. In this paper, we first assess the extent of biased representation of industrialized populations in high profile, international biomedical journals, then compare patterns of morbidity and health across world regions. We also compare demographic rates and the force of selection between subsistence and industrialized populations to reflect on the changes in how selection operates on fertility and survivorship across the lifespan. We argue that, contrary to simplistic misguided solutions like the PaleoDiet, the hypothesis of evolutionary mismatch needs critical consideration of population history, evolutionary biology and evolved reaction norms to prevent and treat diseases. We highlight the critical value of broader sampling by considering the effects of three key exposures that have radically changed over the past century in many parts of the world—pathogen burden, reproductive effort and physical activity—on autoimmune, cardiometabolic and other mismatch diseases.