Is the thrifty genotype hypothesis supported by evidence based on confirmed type 2 diabetes- and obesity-susceptibility variants?

Native Hawaiian and Pacific Islander populations in genomic research

The role of genomic research and medicine in improving health continues to grow significantly, highlighting the need for increased equitable inclusion of diverse populations in genomics. Native Hawaiian and Pacific Islander (NHPI) communities are often missing from these efforts to ensure that the benefits of genomics are accessible to all individuals. In this article, we analyze the qualities of NHPI populations relevant to their inclusion in genomic research and investigate their current representation using data from the genome-wide association studies (GWAS) catalog. A discussion of the barriers NHPI experience regarding participating in research and recommendations to improve NHPI representation in genomic research are also included.

Translational potential of mouse models of human metabolic disease

Obesity causes significant morbidity and mortality globally. Research in the last three decades has delivered a step-change in our understanding of the fundamental mechanisms that regulate energy homeostasis, building on foundational discoveries in mouse models of metabolic disease. However, not all findings made in rodents have translated to humans, hampering drug discovery in this field. Here, we review how studies in mice and humans have informed our current framework for understanding energy homeostasis, discuss their challenges and limitations, and offer a perspective on how human studies may play an increasingly important role in the discovery of disease mechanisms and identification of therapeutic targets in the future.

The complex web of obesity: from genetics to precision medicine

INTRODUCTION

Obesity is a growing public health concern affecting both children and adults. Since it involves both genetic and environmental components, the management of obesity requires both, an understanding of the underlying genetics and changes in lifestyle. The knowledge of obesity genetics will enable the possibility of precision medicine in anti-obesity medications.

AREAS COVERED

Here, we explore health complications and the prevalence of obesity. We discuss disruptions in energy balance as a symptom of obesity, examining evolutionary theories, its multi-factorial origins, and heritability. Additionally, we discuss monogenic and polygenic obesity, the converging biological pathways, potential pharmacogenomics applications, and existing anti-obesity medications - specifically focussing on the leptin-melanocortin and incretin pathways. Comparisons between childhood and adult obesity genetics are made, along with insights into structural variants, epigenetic changes, and environmental influences on epigenetic signatures.

EXPERT OPINION

With recent advancements in anti-obesity drugs, genetic studies pinpoint new targets and allow for repurposing existing drugs. This creates opportunities for genotype-informed treatment options. Also, lifestyle interventions can help in the prevention and treatment of obesity by altering the epigenetic signatures. The comparison of genetic architecture in adults and children revealed a significant overlap. However, more robust studies with diverse ethnic representation is required in childhood obesity.

SH2B1 Tunes Hippocampal ERK Signaling to Influence Fluid Intelligence in Humans and Mice

Fluid intelligence is a cognitive domain that encompasses general reasoning, pattern recognition, and problem-solving abilities independent of task-specific experience. Understanding its genetic and neural underpinnings is critical yet challenging for predicting human development, lifelong health, and well-being. One approach to address this challenge is to map the network of correlations between intelligence and other constructs. In the current study, we performed a genome-wide association study using fluid intelligence quotient scores from the UK Biobank to explore the genetic architecture of the associations between obesity risk and fluid intelligence. Our results revealed novel common genetic loci (SH2B1, TUFM, ATP2A1, and FOXO3) underlying the association between fluid intelligence and body metabolism. Surprisingly, we demonstrated that SH2B1 variation influenced fluid intelligence independently of its effects on metabolism but partially mediated its association with bilateral hippocampal volume. Consistently, selective genetic ablation of Sh2b1 in the mouse hippocampus, particularly in inhibitory neurons, but not in excitatory neurons, significantly impaired working memory, short-term novel object recognition memory, and behavioral flexibility, but not spatial learning and memory, mirroring the human intellectual performance. Single-cell genetic profiling of Sh2B1-regulated molecular pathways revealed that Sh2b1 deletion resulted in aberrantly enhanced extracellular signal-regulated kinase (ERK) signaling, whereas pharmacological inhibition of ERK signaling reversed the associated behavioral impairment. Our cross-species study thus provides unprecedented insight into the role of SH2B1 in fluid intelligence and has implications for understanding the genetic and neural underpinnings of lifelong mental health and well-being.

Genetics: A Starting Point for the Prevention and the Treatment of Obesity

Obesity is a common, serious, and costly disease. More than 1 billion people worldwide are obese-650 million adults, 340 million adolescents, and 39 million children. The WHO estimates that, by 2025, approximately 167 million people-adults and children-will become less healthy because they are overweight or obese. Obesity-related conditions include heart disease, stroke, type 2 diabetes, and certain types of cancer. These are among the leading causes of preventable, premature death. The estimated annual medical cost of obesity in the United States was nearly $173 billion in 2019 dollars. Obesity is considered the result of a complex interaction between genes and the environment. Both genes and the environment change in different populations. In fact, the prevalence changes as the result of eating habits, lifestyle, and expression of genes coding for factors involved in the regulation of body weight, food intake, and satiety. Expression of these genes involves different epigenetic processes, such as DNA methylation, histone modification, or non-coding micro-RNA synthesis, as well as variations in the gene sequence, which results in functional alterations. Evolutionary and non-evolutionary (i.e., genetic drift, migration, and founder's effect) factors have shaped the genetic predisposition or protection from obesity in modern human populations. Understanding and knowing the pathogenesis of obesity will lead to prevention and treatment strategies not only for obesity, but also for other related diseases.

Effects of subtotal pancreatectomy and long-term glucose and lipid overload on insulin secretion and glucose homeostasis in minipigs

INTRODUCTION

Nowadays, there are no strong diabetic pig models, yet they are required for various types of diabetes research. Using cutting-edge techniques, we attempted to develop a type 2 diabetic minipig model in this study by combining a partial pancreatectomy (Px) with an energetic overload administered either orally or parenterally.

METHODS

Different groups of minipigs, including Göttingen-like (GL, n = 17) and Ossabaw (O, n = 4), were developed. Prior to and following each intervention, metabolic assessments were conducted. First, the metabolic responses of the Göttingen-like (n = 3) and Ossabaw (n = 4) strains to a 2-month High-Fat, High-Sucrose diet (HFHSD) were compared. Then, other groups of GL minipigs were established: with a single Px (n = 10), a Px combined with a 2-month HFHSD (n = 6), and long-term intraportal glucose and lipid infusions that were either preceded by a Px (n = 4) or not (n = 4).

RESULTS

After the 2-month HFHSD, there was no discernible change between the GL and O minipigs. The pancreatectomized group in GL minipigs showed a significantly lower Acute Insulin Response (AIR) (18.3 ± 10.0 IU/mL after Px vs. 34.9 ± 13.7 IU/mL before, p < .0005). In both long-term intraportal infusion groups, an increase in the Insulinogenic (IGI) and Hepatic Insulin Resistance Indexes (HIRI) was found with a decrease in the AIR, especially in the pancreatectomized group (IGI: 4.2 ± 1.9 after vs. 1.5 ± 0.8 before, p < .05; HIRI (×10^-5 ): 12.6 ± 7.9 after vs. 3.8 ± 4.3 before, p < .05; AIR: 24.4 ± 13.7 µIU/mL after vs. 43.9 ± 14.5 µIU/mL before, p < .005). Regardless of the group, there was no fasting hyperglycemia.

CONCLUSIONS

In this study, we used pancreatectomy followed by long-term intraportal glucose and lipid infusions to develop an original minipig model with metabolic syndrome and early signs of glucose intolerance. We reaffirm the pig's usefulness as a preclinical model for the metabolic syndrome but without the fasting hyperglycemia that characterizes diabetes mellitus.

Understanding the contemporary high obesity rate from an evolutionary genetic perspective

The topic of obesity is gaining increasing popularity globally. From an evolutionary genetic perspective, it is believed that the main cause of the high obesity rate is the mismatch between environment and genes after people have shifted toward a modern high-calorie diet. However, it has been debated for over 60 years about how obesity-related genes become prevalent all over the world. Here, we review the three most influential hypotheses or viewpoints, i.e., the thrifty gene hypothesis, the drifty gene hypothesis, and the maladaptation viewpoint. In particular, genome-wide association studies in the recent 10 years have provided rich findings and evidence to be considered for a better understanding of the evolutionary genetic mechanisms of obesity. We anticipate this brief review to direct further studies and inspire the future application of precision medicine in obesity treatment.

Obesity: an evolutionary context

People completely lacking body fat (lipodystrophy/lipoatrophy) and those with severe obesity both show profound metabolic and other health issues. Regulating levels of body fat somewhere between these limits would, therefore, appear to be adaptive. Two different models might be contemplated. More traditional is a set point (SP) where the levels are regulated around a fixed level. Alternatively, dual-intervention point (DIP) is a system that tolerates fairly wide variation but is activated when critically high or low levels are breached. The DIP system seems to fit our experience much better than an SP, and models suggest that it is more likely to have evolved. A DIP system may have evolved because of two contrasting selection pressures. At the lower end, we may have been selected to avoid low levels of fat as a buffer against starvation, to avoid disease-induced anorexia, and to support reproduction. At the upper end, we may have been selected to avoid excess storage because of the elevated risks of predation. This upper limit of control seems to have malfunctioned because some of us deposit large fat stores, with important negative health effects. Why has evolution not protected us against this problem? One possibility is that the protective system slowly fell apart due to random mutations after we dramatically reduced the risk of being predated during our evolutionary history. By chance, it fell apart more in some people than others, and these people are now unable to effectively manage their weight in the face of the modern food glut. To understand the evolutionary context of obesity, it is important to separate the adaptive reason for storing some fat (i.e. the lower intervention point), from the nonadaptive reason for storing lots of fat (a broken upper intervention point). The DIP model has several consequences, showing how we understand the obesity problem and what happens when we attempt to treat it.

Epidemiology of Type 2 Diabetes in Indigenous Communities in the United States

PURPOSE OF REVIEW

The present review focuses on the epidemiology of type 2 diabetes (T2D) in Indigenous communities in the continental United States (U.S.)-including disease prevention and management-and discusses special considerations in conducting research with Indigenous communities.

RECENT FINDINGS

Previous studies have reported the disparately high prevalence of diabetes, especially T2D, among Indigenous peoples in the U.S. The high prevalence and incidence of early-onset T2D in Indigenous youth relative to that of all youth in the U.S. population pose challenges to the prevention of complications of diabetes. Behavioral, dietary, lifestyle, and genetic factors associated with T2D in Indigenous communities are often investigated. More limited is the discussion of the historical and ongoing consequences of colonization and displacement that impact the aforementioned risk factors. Future research is necessary to assess community-specific needs with respect to diabetes prevention and management across the diversity of Indigenous communities in the U.S.

Analysis of Evolution and Ethnic Diversity at Glucose-Associated SNPs of Circadian Clock-Related Loci with Cryptochrome 1, Cryptochrome 2, and Melatonin receptor 1B

Diabetes shows high heritability and, worldwide, causes significant health problems including cardiovascular disease and stroke. There is significant variation in the frequency of diabetes between different populations. Both Cryptochromes and Melatonin have a major role to regulate the circadian clock. Circadian clock failure causes metabolic dysfunctions including diabetes and obesity. Variations in the Cryptochrome 1, the Cryptochrome 2, and the Melatonin receptor 1B (MTNR1B) genes show associations with fasting glucose, and are also related to circadian clock. Here, we analyzed evidence for genetic selection and ethnic diversity at circadian clock- and glucose-related gene loci associated with Cryptochrome 1, Cryptochrome 2, and MTNR1B. We carried out a 3-step genetic method to investigate genetic selection at the Cryptochrome 1, Cryptochrome 2, and MTNR1B on four populations from the 1000 Genomes Project and HapMap. First we used F-statistics to quantify genetic population differences and find ethnic diversity. Then we applied a long-range haplotype test to detect significant extreme long haplotypes, and then the integrated haplotype score (iHS) to find genetic selection at Cryptochrome 1, Cryptochrome 2, and MTNR1B. We observed genetic population differences and ethnic diversity at one glucose-associated Cryptochrome 1 single-nucleotide polymorphism (SNP) (rs8192440), one glucose-associated Cryptochrome 2 SNP (rs11605924), and one glucose-associated MTNR1B SNP (rs10830963) by F-statistics. Both Cryptochrome 1 and MTNR1B also showed selection by the iHS. These observations show new evidence for evolution at Cryptochrome 1, Cryptochrome 2 and MTNR1B. Further investigation should continue to examine the evolution of circadian clock- and glucose-related genes.

Metabolic Diseases and Down Syndrome: How Are They Linked Together?

Down syndrome is a genetic disorder caused by the presence of a third copy of chromosome 21, associated with intellectual disabilities. Down syndrome is associated with anomalies of both the nervous and endocrine systems. Over the past decades, dramatic advances in Down syndrome research and treatment have helped to extend the life expectancy of these patients. Improved life expectancy is obviously a positive outcome, but it is accompanied with the need to address previously overlooked complications and comorbidities of Down syndrome, including obesity and diabetes, in order to improve the quality of life of Down syndrome patients. In this focused review, we describe the associations between Down syndrome and comorbidities, obesity and diabetes, and we discuss the understanding of proposed mechanisms for the association of Down syndrome with metabolic disorders. Drawing molecular mechanisms through which Type 1 diabetes and Type 2 diabetes could be linked to Down syndrome could allow identification of novel drug targets and provide therapeutic solutions to limit the development of metabolic and cognitive disorders.

Deciphering Biochemical and Molecular Signatures Associated with Obesity in Context of Metabolic Health

This study aims to identify the clinical and genetic markers related to the two uncommon nutritional statuses—metabolically unhealthy normal-weight (MUNW) and metabolically healthy overweight/obese (MHOW) individuals in the physically active individuals. Physically active male volunteers (n = 120) were recruited, and plasma samples were analyzed for the clinical parameters. Triglycerides, HDL-Cholesterol, LDL-cholesterol, total cholesterol, C-reactive protein, and insulin resistance were considered as markers of metabolic syndrome. The subjects were classified as ‘healthy’ (0 metabolic abnormalities) or ‘unhealthy’ (≥1 metabolic abnormalities) in their respective BMI group with a cut-off at 24.9 kg/m². Analysis of biochemical variables was done using enzyme linked immunosorbent assay (ELISA) kits with further confirmation using western blot analysis. The microarray was conducted, followed by quantitative real-time PCR to identify and analyze differentially expressed genes (DEGs). The MHOW group constituted 12.6%, while the MUNW group constituted 32.4% of the total study population. Pro-inflammatory markers like interleukin-6, tumor necrosis factor (TNF)-α, and ferritin were increased in metabolically unhealthy groups in comparison to metabolically healthy groups. Gene expression profiling of MUNW and MHOW individuals resulted in differential expression of 7470 and 5864 genes, respectively. The gene ontology (GO) biological pathway analysis showed significant enrichment of the ‘JAK/STAT signaling pathway’ in MUNW and ‘The information-processing pathway at the IFN-β enhancer′ pathway in MHOW. The G6PC3 gene has genetically emerged as a new distinct gene showing its involvement in insulin resistance. Biochemical, as well as genetic analysis, revealed that MUNW and MHOW are the transition state between healthy and obese individuals with simply having fewer metabolic abnormalities. Moreover, it is possible that the state of obesity is a biological adaptation to cope up with the unhealthy parameters.

Analysis of genetic selection at insulin receptor substrate-2 gene loci

Purpose

Type 2 diabetes mellitus (T2DM) is highly heritable and exhibits significant variability in prevalence between different populations. Prevalence of T2DM is higher in Asian and African relative to European populations. During evolution, traditional feast-famine cycles likely led to significant natural selection impacting metabolic genes. Human adaptation to environmental changes (food supply, lifestyle, climate, and geography) likely influenced differential selection of T2DM-associated genes. Together, insulin receptor substrate-1 and -2 (IRS1 and IRS2) genes encode the major ligands of insulin and IGF1 receptors. Irs2-deficient mice exhibit a T2DM phenotype with severe insulin resistance, and a common IRS2 polymorphism is associated with T2DM. Therefore, the present study sought evidence of natural selection at IRS2 loci.

Methods

Data were sourced from the HapMap and 1000 Genomes projects, comprising four different populations with distinct ancestries: European, Yoruba, Han Chinese, and Japanese. A three-step method was applied to detect IRS2 locus selection. The long-range haplotype (LRH) test detected unusual extended haplotypes, the integrated haplotype score (iHS) detected selection, and Wright's F-statistics (particularly Wright's fixation index: F_ST) were calculated as a measure of population differentiation.

Results

The African population exhibited highly significant LRH findings (percentile >99.9, p = 0.005-0.0009), while both the European and African populations exhibited extreme positive iHS test scores ([iHS] >2.5).

Conclusion

These findings indicate that genetic selection has occurred at the IRS2 locus, warranting further research into the adaptive evolution of metabolic disorder-associated genes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40200-021-00745-y.

Assessment of the potential role of natural selection in type 2 diabetes and related traits across human continental ancestry groups: comparison of phenotypic with genotypic divergence

AIMS/HYPOTHESIS

Prevalence of type 2 diabetes differs among human ancestry groups, and many hypotheses invoke differential natural selection to account for these differences. We sought to assess the potential role of differential natural selection across major continental ancestry groups for diabetes and related traits, by comparison of genetic and phenotypic differences.

METHODS

This was a cross-sectional comparison among 734 individuals from an urban sample (none of whom was more closely related to another than third-degree relatives), including 83 African Americans, 523 American Indians and 128 European Americans. Participants were not recruited based on diabetes status or other traits. BMI was calculated, and diabetes was diagnosed by a 75 g oral glucose tolerance test. In those with normal glucose tolerance (n = 434), fasting insulin and 30 min post-load insulin, adjusted for 30 min glucose, were taken as measures of insulin resistance and secretion, respectively. Whole exome sequencing was performed, resulting in 97,388 common (minor allele frequency ≥ 5%) variants; the coancestry coefficient (F_ST) was calculated across all markers as a measure of genetic divergence among ancestry groups. The phenotypic divergence index (P_ST) was also calculated from the phenotypic differences and heritability (which was estimated from genetic relatedness calculated empirically across all markers in 761 American Indian participants prior to the exclusion of close relatives). Under evolutionary neutrality, the expectation is P_ST = F_ST, while for traits under differential selection P_ST is expected to be significantly greater than F_ST. A bootstrap procedure was used to test the hypothesis P_ST = F_ST. RESULTS: With adjustment for age and sex, prevalence of type 2 diabetes was 34.0% in American Indians, 12.4% in African Americans and 10.4% in European Americans (p = 2.9 × 10^-10 for difference among groups). Mean BMI was 36.3, 33.4 and 33.0 kg/m², respectively (p = 1.9 × 10^-7). Mean fasting insulin was 63.8, 48.4 and 45.2 pmol/l (p = 9.2 × 10^-5), while mean 30 min insulin was 559.8, 553.5 and 358.8 pmol/l, respectively (p = 5.7 × 10^-8). F_ST across all markers was 0.130, while P_ST for liability to diabetes, adjusted for age and sex, was 0.149 (p = 0.35 for difference with F_ST). P_ST was 0.094 for BMI (p = 0.54), 0.095 for fasting insulin (p = 0.54) and 0.216 (p = 0.18) for 30 min insulin. For type 2 diabetes and BMI, the maximum divergence between populations was observed between American Indians and European Americans (P_ST-MAX = 0.22, p = 0.37, and P_ST-MAX = 0.14, p = 0.61), which suggests that a relatively modest 22% or 14% of the genetic variance, respectively, can potentially be explained by differential selection (assuming the absence of neutral drift).

CONCLUSIONS/INTERPRETATION

These analyses suggest that while type 2 diabetes and related traits differ significantly among continental ancestry groups, the differences are consistent with neutral expectations based on heritability and genetic distances. While these analyses do not exclude a modest role for natural selection, they do not support the hypothesis that differential natural selection is necessary to explain the phenotypic differences among these ancestry groups. Graphical abstract.

The Role of RNA Editing in Cancer Development and Metabolic Disorders

Numerous human diseases arise from alterations of genetic information, most notably DNA mutations. Thought to be merely the intermediate between DNA and protein, changes in RNA sequence were an afterthought until the discovery of RNA editing 30 years ago. RNA editing alters RNA sequence without altering the sequence or integrity of genomic DNA. The most common RNA editing events are A-to-I changes mediated by adenosine deaminase acting on RNA (ADAR), and C-to-U editing mediated by apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1 (APOBEC1). Both A-to-I and C-to-U editing were first identified in the context of embryonic development and physiological homeostasis. The role of RNA editing in human disease has only recently started to be understood. In this review, the impact of RNA editing on the development of cancer and metabolic disorders will be examined. Distinctive functions of each RNA editase that regulate either A-to-I or C-to-U editing will be highlighted in addition to pointing out important regulatory mechanisms governing these processes. The potential of developing novel therapeutic approaches through intervention of RNA editing will be explored. As the role of RNA editing in human disease is elucidated, the clinical utility of RNA editing targeted therapies will be needed. This review aims to serve as a bridge of information between past findings and future directions of RNA editing in the context of cancer and metabolic disease.

Revisiting the evolutionary origins of obesity: lazy versus peppy-thrifty genotype hypothesis

The recent global obesity epidemic is attributed to major societal and environmental changes, such as excessive energy intake and sedentary lifestyle. However, exposure to 'obesogenic' environments does not necessarily result in obesity at the individual level, as 40-75% of body mass index variation in population is attributed to genetic differences. The thrifty genotype theory posits that genetic variants promoting efficient food sequestering and optimal deposition of fat during periods of food abundance were evolutionarily advantageous for the early hunter-gatherer and were positively selected. However, the thrifty genotype is likely too simplistic and fails to provide a justification for the complex distribution of obesity predisposing gene variants and for the broad range of body mass index observed in diverse ethnic groups. This review proposes that gene pleiotropy may better account for the variability in the distribution of obesity susceptibility alleles across modern populations. We outline the lazy-thrifty versus peppy-thrifty genotype hypothesis and detail the body of evidence in the literature in support of this novel concept. Future population genetics and mathematical modelling studies that account for pleiotropy may further improve our understanding of the evolutionary origins of the current obesity epidemic.

Transferred maternal fatty acids stimulate fetal adipogenesis and lead to neonatal and adult obesity

The prevalence of adult and childhood obesity are increasing. Most of the human newborn's body fat accumulates in the last half of intrauterine life. Fat in the fetus was thought to be mostly synthesized from glucose, but now it is commonly accepted that the bulk of it is the product of placental transfer of maternal fatty acids. Transported fatty acids originate in maternal plasma "free" fatty acids, fatty acids hydrolyzed from maternal plasma triglycerides, and the poly-unsaturated fatty acid component of maternal phospholipids. Glucose remains an important precursor of alpha-glycerol phosphate, to which most transported fatty acids are eventually esterified. Maternal plasma lipids are elevated in late pregnancy and even more in obese and diabetic pregnant women. This accelerates the placental transport of fatty acids. The hypothesis presented in this paper rests on the observations that the exponential increase in fat tissue in the human embryo's body occurs in time to parallel the increase of lipids in the mother's blood and depends on the chemical affinity of the transcription factor PPAR gamma to fatty acids and on fatty acid stimulation of adipocyte generation from precursor cells. The hypothesis asserts that transported maternal fatty acids activate the transcription factors in the fetus and initiate conversion of the mesenchymal stem cells into adipocytes. In obese and diabetic mothers, the higher plasma lipids facilitate increased placental fatty acid transfer. This will increase adipocyte generation and, through this, the prevalence of babies with increased fat cell size and number. Babies born with increased adipose tissue cellularity will have greater probability of growing up to become obese adolescents and adults. These newborns, whose obesity is hyperplastic as well as hypertrophic, as adults will have difficulty losing weight through diet and exercise or will regain the lost weight more quickly than others without these characteristics. Accordingly, increased placental fatty acid transfer and accelerated adipocyte generation may explain not only neonatal obesity, but some aspects of the adult obesity epidemic also. It is therefore recommended that prevention of fetal fat cell hyperplasia, by lowering maternal plasma lipids in mid and late pregnancy, should be attempted in pregnancies at risk for macrosomia.

Commentary: The Invention of Aboriginal Diabetes: The Role of the Thrifty Gene Hypothesis in Canadian Health Care Provision

The purpose of this study was to analyze the extent to which the 'thrifty gene hypothesis' remains embedded within regimes of Canadian health care. The thrifty gene hypothesis, formulated by the American geneticist and travelling scientist James V. Neel in 1962, proposed that Indigenous peoples were genetically predisposed to Type 2 diabetes due to the foodways of their ancestors. The hypothesis was functionally racist and based on what biological anthropologists now call 'the myth of forager food insecurity.' Importantly, Neel reconsidered his own hypothesis in 1982 before he ultimately rejected it in 1999; nonetheless, in the mid-1990s, a team of Canadian scientists led by the endocrinologist Robert Hegele of Western University conducted a genetic study on the OjiCree community of Sandy Lake First Nation in northern Ontario. Thereafter, Hegele told the academic world and news media that he had discovered a thrifty gene in Sandy Lake. Like Neel, Hegele later came to reject his own study in 2011. Nonetheless, the 'thrifty gene hypothesis' and Hegele's Sandy Lake study continue to be cited, referenced, and reproduced in the current Clinical Guidelines of the Canadian Diabetes Association, as well as across state-related health literature more broadly. The purpose of this study, then, will be to apply the PHCRP to the thrifty gene hypothesis in a Canadian context.

The evolution of body fatness: trading off disease and predation risk

Human obesity has a large genetic component, yet has many serious negative consequences. How this state of affairs has evolved has generated wide debate. The thrifty gene hypothesis was the first attempt to explain obesity as a consequence of adaptive responses to an ancient environment that in modern society become disadvantageous. The idea is that genes (or more precisely, alleles) predisposing to obesity may have been selected for by repeated exposure to famines. However, this idea has many flaws: for instance, selection of the supposed magnitude over the duration of human evolution would fix any thrifty alleles (famines kill the old and young, not the obese) and there is no evidence that hunter-gatherer populations become obese between famines. An alternative idea (called thrifty late) is that selection in famines has only happened since the agricultural revolution. However, this is inconsistent with the absence of strong signatures of selection at single nucleotide polymorphisms linked to obesity. In parallel to discussions about the origin of obesity, there has been much debate regarding the regulation of body weight. There are three basic models: the set-point, settling point and dual-intervention point models. Selection might act against low and high levels of adiposity because food unpredictability and the risk of starvation selects against low adiposity whereas the risk of predation selects against high adiposity. Although evidence for the latter is quite strong, evidence for the former is relatively weak. The release from predation ∼2-million years ago is suggested to have led to the upper intervention point drifting in evolutionary time, leading to the modern distribution of obesity: the drifty gene hypothesis. Recent critiques of the dual-intervention point/drifty gene idea are flawed and inconsistent with known aspects of energy balance physiology. Here, I present a new formulation of the dual-intervention point model. This model includes the novel suggestion that food unpredictability and starvation are insignificant factors driving fat storage, and that the main force driving up fat storage is the risk of disease and the need to survive periods of pathogen-induced anorexia. This model shows why two independent intervention points are more likely to evolve than a single set point. The molecular basis of the lower intervention point is likely based around the leptin pathway signalling. Determining the molecular basis of the upper intervention point is a crucial key target for future obesity research. A potential definitive test to separate the different models is also described.

On the origin of obesity: identifying the biological, environmental and cultural drivers of genetic risk among human populations

Genetic predisposition to obesity presents a paradox: how do genetic variants with a detrimental impact on human health persist through evolutionary time? Numerous hypotheses, such as the thrifty genotype hypothesis, attempt to explain this phenomenon yet fail to provide a justification for the modern obesity epidemic. In this critical review, we appraise existing theories explaining the evolutionary origins of obesity and explore novel biological and sociocultural agents of evolutionary change to help explain the modern-day distribution of obesity-predisposing variants. Genetic drift, acting as a form of 'blind justice,' may randomly affect allele frequencies across generations while gene pleiotropy and adaptations to diverse environments may explain the rise and subsequent selection of obesity risk alleles. As an adaptive response, epigenetic regulation of gene expression may impact the manifestation of genetic predisposition to obesity. Finally, exposure to malnutrition and disease epidemics in the wake of oppressive social systems, culturally mediated notions of attractiveness and desirability, and diverse mating systems may play a role in shaping the human genome. As an important first step towards the identification of important drivers of obesity gene evolution, this review may inform empirical research focused on testing evolutionary theories by way of population genetics and mathematical modelling.

Ethnic and population differences in the genetic predisposition to human obesity

Obesity rates have escalated to the point of a global pandemic with varying prevalence across ethnic groups. These differences are partially explained by lifestyle factors in addition to genetic predisposition to obesity. This review provides a comprehensive examination of the ethnic differences in the genetic architecture of obesity. Using examples from evolution, heritability, admixture, monogenic and polygenic studies of obesity, we provide explanations for ethnic differences in the prevalence of obesity. The debate over definitions of race and ethnicity, the advantages and limitations of multi-ethnic studies and future directions of research are also discussed. Multi-ethnic studies have great potential to provide a better understanding of ethnic differences in the prevalence of obesity that may result in more targeted and personalized obesity treatments.

A global evolutionary and metabolic analysis of human obesity gene risk variants

It is generally accepted that the selection of gene variants during human evolution optimized energy metabolism that now interacts with our obesogenic environment to increase the prevalence of obesity. The purpose of this study was to perform a global evolutionary and metabolic analysis of human obesity gene risk variants (110 human obesity genes with 127 nearest gene risk variants) identified using genome-wide association studies (GWAS) to enhance our knowledge of early and late genotypes. As a result of determining the mean frequency of these obesity gene risk variants in 13 available populations from around the world our results provide evidence for the early selection of ancestral risk variants (defined as selection before migration from Africa) and late selection of derived risk variants (defined as selection after migration from Africa). Our results also provide novel information for association of these obesity genes or encoded proteins with diverse metabolic pathways and other human diseases. The overall results indicate a significant differential evolutionary pattern for the selection of obesity gene ancestral and derived risk variants proposed to optimize energy metabolism in varying global environments and complex association with metabolic pathways and other human diseases. These results are consistent with obesity genes that encode proteins possessing a fundamental role in maintaining energy metabolism and survival during the course of human evolution.

Examining How Our Shared Evolutionary History Shapes Future Disease Outcomes

Cardiometabolic diseases are major contributors to mortality and morbidity, and their burden displays global and regional disparities. Gene-environment interactions contribute to the pathogenesis of cardiometabolic diseases. Population differences in genetic structure, ancient environmental pressures that shape the human genome, and early life environmental adversities (e.g., in utero conditions) all contribute to observed disparities in global cardiometabolic diseases. The genetic and sociocultural diversity of global populations presents opportunities for discovering genomic loci that influence cardiometabolic diseases as illustrated by a few genetic, epigenetic, and population-genetic discoveries leading to notable understanding of disease mechanisms. However, African, Latin American and Hispanic, and indigenous peoples represent <4% of all genome-wide association study samples analyzed to date. Using examples of recent studies in African populations, we discuss the crucial importance of conducting genomic studies in ancestrally diverse populations to understand disease mechanisms and to prepare fertile ground for future delivery of precise health care to all individuals.

Analysis of Positive Selection at Single Nucleotide Polymorphisms Associated with Body Mass Index Does Not Support the "Thrifty Gene" Hypothesis

The "thrifty gene hypothesis" suggests genetic susceptibility to obesity arises because of positive selection for alleles that favored fat deposition and survival during famines. We used public domain data to locate signatures of positive selection based on derived allele frequency, genetic diversity, long haplotypes, and differences between populations at SNPs identified in genome-wide association studies (GWASs) for BMI. We used SNPs near the lactase (LCT), SLC24A5, and SLC45A2 genes as positive controls and 120 randomly selected SNPs as negative controls. We found evidence for positive selection (p < 0.05) at nine out of 115 BMI SNPs. However, five of these involved positive selection for the protective allele (i.e., for leanness). The widespread absence of signatures of positive selection, combined with selection favoring leanness at some alleles, does not support the suggestion that obesity provided a selective advantage to survive famines, or any other selective advantage.

Irrational use of antibiotics and the risk of diabetes in Ghana

Epidemiological studies show clearly that Caesarean birth, perinatal or neonatal irrational antibiotic use is strongly associated with increased risk of obesity and diabetes in later life. Irrational use of antibiotics is a great global public health concern especially in developing economies like Ghana due to poor regulation on medicines. Unfortunately, this concern has been reduced to the fear of development of resistant organisms and the destruction of the world's limited range of antibiotics therapy at the expense of other insidious risks including the development of metabolic and atopic diseases. These risks however appear to have greater implications on public health systems of developing economies. Here, we review the ignored role of antibiotics in the global obesity pandemic and project the risk that it poses to the health system of a developing economy like Ghana.

FUNDING

Department of Pharmacology, College of Health Sciences, Kwame Nkrumah university of Science and Technology, Kumasi, Ghana.

Evidence of Polygenic Adaptation in the Systems Genetics of Anthropometric Traits

Many signals of natural selection have been identified in the human genome. However, except for some single-locus mechanisms, most molecular processes generating these adaptation signals are still unknown. We developed an approach that integrates datasets related to genome-wide association studies (GWAS) with information about systems biology and genetic signatures of natural selection to identify evidence of polygenic adaptation. Specifically, we focused on five anthropometric measurements: body mass index (BMI), height, waist-to-hip ratio adjusted for BMI (WHR), and waist circumference adjusted for BMI (WC), and sex differences for WHR and WC. We performed an enrichment analysis for signals of natural selection in protein interaction networks associated with anthropometric traits in European populations. The adaptation signals-enriched gene networks associated highlighted epistatic interactions in the context of polygenic selection for the investigated traits. These polygenic mechanisms indicated intriguing selective mechanisms related to the anthropometric traits: adult locomotory behavior for BMI, infection resistance for height, interplay between lipid transport and immune systems for WHR, and female-specific polygenic adaptation for WHR and WC. In conclusion, we observed evidence of polygenic adaptation in the context of systems genetics of anthropometric traits that indicates polygenic mechanisms related to the natural selection in European populations.

Evidence for natural selection at the melanocortin-3 receptor gene in European and African populations

AIMS

Obesity is increasing steadily in worldwide prevalence and is known to cause serious health problems in association with type 2 diabetes mellitus (T2DM), including hypertension, stroke, and cardiovascular diseases. According to the thrifty gene hypothesis, the natural selection of obesity-related genes is important during feast and famine because they control body weight and fat levels. Past human adaptations to environmental changes in food supply, lifestyle, and geography may have influenced the selection of genes associated with the metabolism of glucose, lipids, and energy. The melanocortin-3 receptor gene (MC3R) is associated with obesity, with MC3R-deficient mice showing increased fat mass. MC3R variations are also linked with childhood obesity and insulin resistance. Here, we aimed to uncover evidence of selection at MC3R.

METHODS

We performed a three-step method to detect selection at MC3R using HapMap population data. We used Wright's F statistics as a measure of population differentiation, the long-range haplotype test to identify extended haplotypes, and the integrated haplotype score (iHS) to detect selection at MC3R.

RESULTS

We observed high population differentiation between European and African populations at two MC3R childhood obesity- and insulin resistance-associated single-nucleotide polymorphisms (rs3746619 and rs3827103) using Wright's F statistics. The iHS revealed evidence of natural selection at MC3R.

CONCLUSIONS

These findings provide evidence for natural selection at MC3R. Further investigation is warranted into adaptive evolution at T2DM- and obesity-associated genes.

Evolutionary triangulation: informing genetic association studies with evolutionary evidence

Genetic studies of human diseases have identified many variants associated with pathogenesis and severity. However, most studies have used only statistical association to assess putative relationships to disease, and ignored other factors for evaluation. For example, evolution is a factor that has shaped disease risk, changing allele frequencies as human populations migrated into and inhabited new environments. Since many common variants differ among populations in frequency, as does disease prevalence, we hypothesized that patterns of disease and population structure, taken together, will inform association studies. Thus, the population distributions of allelic risk variants should reflect the distributions of their associated diseases. Evolutionary Triangulation (ET) exploits this evolutionary differentiation by comparing population structure among three populations with variable patterns of disease prevalence. By selecting populations based on patterns where two have similar rates of disease that differ substantially from a third, we performed a proof of principle analysis for this method. We examined three disease phenotypes, lactase persistence, melanoma, and Type 2 diabetes mellitus. We show that for lactase persistence, a phenotype with a simple genetic architecture, ET identifies the key gene, lactase. For melanoma, ET identifies several genes associated with this disease and/or phenotypes related to it, such as skin color genes. ET was less obviously successful for Type 2 diabetes mellitus, perhaps because of the small effect sizes in known risk loci and recent environmental changes that have altered disease risk. Alternatively, ET may have revealed new genes involved in conferring disease risk for diabetes that did not meet nominal GWAS significance thresholds. We also compared ET to another method used to filter for phenotype associated genes, population branch statistic (PBS), and show that ET performs better in identifying genes known to associate with diseases appropriately distributed among populations. Our results indicate that ET can filter association results to improve our ability to discover disease loci.

Physical activity and genetic predisposition to obesity in a multiethnic longitudinal study

Physical activity (PA) has been shown to reduce the impact of FTO variation and obesity genetic risk scores (GRS) on BMI. We examined this interaction using a quantitative measure of PA and two adiposity indexes in a longitudinal multi-ethnic study. We analyzed the impact of PA on the association between 14 obesity predisposing variants (analyzed independently and as a GRS) and baseline/follow-up obesity measures in the multi-ethnic prospective cohort EpiDREAM (17423 participants from six ethnic groups). PA was analyzed using basic (low-moderate-high) and quantitative measures (metabolic equivalents (METS)), while BMI and the body adiposity index (BAI) were used to measure obesity. Increased PA was associated with decreased BMI/BAI at baseline/follow-up. FTO rs1421085, CDKAL1 rs2206734, TNNl3K rs1514176, GIPR rs11671664 and the GRS were associated with obesity measures at baseline and/or follow-up. Risk alleles of three SNPs displayed nominal associations with increased (NTRK2 rs1211166, BDNF rs1401635) or decreased (NPC1 rs1805081) basic PA score independently of BMI/BAI. Both basic and quantitative PA measures attenuated the association between FTO rs1421085 risk allele and BMI/BAI at baseline and follow-up. Our results show that physical activity can blunt the genetic effect of FTO rs1421085 on adiposity by 36–75% in a longitudinal multi-ethnic cohort.

Intrauterine Programming of Diabetes and Adiposity

The prevalence of diabetes and adiposity has increased at an alarming rate and together they contribute to the rise in morbidity and mortality worldwide. Genetic studies till date have succeeded in explaining only a proportion of heritability, while a major component remains unexplained. Early life determinants of future risk of these diseases are likely contributors to the missing heritability and thus have a significant potential in disease prevention. Epidemiological and animal studies show the importance of intrauterine and early postnatal environment in programming of the fetus to adverse metabolic outcomes and support the notion of Developmental Origins of Health and Disease (DOHaD). Emerging evidence highlights the role of epigenetic mechanisms in mediating effects of environmental exposures, which in certain instances may exhibit intergenerational transmission even in the absence of exposure. In this article, we will discuss the complexity of diabetes and increased adiposity and mechanisms of programming of these adverse metabolic conditions.

Pacific Populations, Metabolic Disease and 'Just-So Stories': A Critique of the 'Thrifty Genotype' Hypothesis in Oceania

Pacific populations have long been observed to suffer a high burden of metabolic disease, including obesity, type 2 diabetes and gout. The 'Thrifty Genotype' hypothesis has frequently been used to explain this high prevalence of disease. Here, the 'Thrifty Genotype' hypothesis and the evolutionary background of Pacific populations are examined. We question its relevance not only in the Pacific region but more generally. Not only has the hypothesis not been explicitly tested, but most archaeological and anthropological data from the Pacific fundamentally do not support its application.

β cell dysfunction versus insulin resistance in the pathogenesis of type 2 diabetes in East Asians

Type 2 diabetes (T2DM) is one of the most serious global health problems and is mainly a result of the drastic increase in East Asia, which includes over a fourth of the global diabetes population. Lifestyle factors and ethnicity are two determinants in the etiology of T2DM, and lifestyle changes such as higher fat intake and less physical activity link readily to T2DM in East Asians. It is widely recognized that T2DM in East Asians is characterized primarily by β cell dysfunction, which is evident immediately after ingestion of glucose or meal, and less adiposity compared to the disease in Caucasians. These pathophysiological differences have an important impact on therapeutic approaches. Here, we revisit the pathogenesis of T2DM in light of β cell dysfunction versus insulin resistance in East Asians and discuss ethnic differences in the contributions of insulin secretion and insulin resistance, together with incretin secretin and action, to glucose intolerance.

Genetic Determinants of Type 2 Diabetes in Asians

Type 2 diabetes (T2D) has become a major health problem throughout the world and the epidemic is particularly severe in Asian countries. Compared with European populations, Asians tend to develop diabetes at a younger age and at much higher incidence rates given the same amount of weight gain. Genome-wide association studies (GWAS) have identified over 70 loci associated with T2D. Although the majority of GWAS results were conducted in populations of European ancestry, recent GWAS in Asians have made important contributions to the identification of T2D susceptibility loci. These studies not only confirmed T2D susceptibility loci initially identified in European populations, but also identified novel susceptibility loci that provide new insights into the pathophysiology of diseases. In this article, we review GWAS results of T2D conducted in East and South Asians and compare them to those of European populations. Currently identified T2D genetic variants do not appear to explain the phenomenon that Asians are more susceptible to T2D than European populations, suggesting further studies in Asian populations are needed.

Signatures of natural selection at the FTO (fat mass and obesity associated) locus in human populations

Background and aims

Polymorphisms in the first intron of FTO have been robustly replicated for associations with obesity. In the Sorbs, a Slavic population resident in Germany, the strongest effect on body mass index (BMI) was found for a variant in the third intron of FTO (rs17818902). Since this may indicate population specific effects of FTO variants, we initiated studies testing FTO for signatures of selection in vertebrate species and human populations.

Methods

First, we analyzed the coding region of 35 vertebrate FTO orthologs with Phylogenetic Analysis by Maximum Likelihood (PAML, ω = dN/dS) to screen for signatures of selection among species. Second, we investigated human population (Europeans/CEU, Yoruba/YRI, Chinese/CHB, Japanese/JPT, Sorbs) SNP data for footprints of selection using DnaSP version 4.5 and the Haplotter/PhaseII. Finally, using ConSite we compared transcription factor (TF) binding sites at sequences harbouring FTO SNPs in intron three.

Results

PAML analyses revealed strong conservation in coding region of FTO (ω<1). Sliding-window results from population genetic analyses provided highly significant (p<0.001) signatures for balancing selection specifically in the third intron (e.g. Tajima’s D in Sorbs = 2.77). We observed several alterations in TF binding sites, e.g. TCF3 binding site introduced by the rs17818902 minor allele.

Conclusion

Population genetic analysis revealed signatures of balancing selection at the FTO locus with a prominent signal in intron three, a genomic region with strong association with BMI in the Sorbs. Our data support the hypothesis that genes associated with obesity may have been under evolutionary selective pressure.

The ethnoepidemiology of obesity

The prevalence of overweight and obesity varies significantly across ethnic groups and among aboriginal people in Canada and appears to be increasing overall in children and youth, which will have significant health consequences in the future. Individual health behaviours, genetic predisposition, and community-level factors all contribute to the high burden of overweight and obesity across communities in Canada. Preliminary studies indicate that individuals who live in neighbourhoods in Canada with increased walkability, fewer fast food outlets, and higher socioeconomic status have lower rates of overweight/obesity when compared with other neighbourhoods. However, more research is required to understand the impact of community level factors on overweight/obesity trends in Canadian ethnic groups, including children and youth, and aboriginal people.

Can evidence from genome-wide association studies and positive natural selection surveys be used to evaluate the thrifty gene hypothesis in East Asians?

Body fat deposition and distribution differ between East Asians and Europeans, and for the same level of obesity, East Asians are at higher risks of Type 2 diabetes (T2D) and other metabolic disorders. This observation has prompted the reclassifications of body mass index thresholds for the definitions of “overweight” and “obese” in East Asians. However, the question remains over what evolutionary mechanisms have driven the differences in adiposity morphology between two population groups that shared a common ancestor less than 80,000 years ago. The Thrifty Gene hypothesis has been suggested as a possible explanation, where genetic factors that allowed for efficient food-energy conversion and storage are evolutionarily favoured by conferring increased chances of survival and fertility. Here, we leveraged on the existing findings from genome-wide association studies and large-scale surveys of positive natural selection to evaluate whether there is currently any evidence to support the Thrifty Gene hypothesis. We first assess whether the existing genetic associations with obesity and T2D are located in genomic regions that are reported to be under positive selection, and if so, whether the risk alleles sit on the extended haplotype forms. In addition, we interrogate whether these risk alleles are the derived forms that differ from the ancestral alleles, and whether there is significant evidence of population differentiation at these SNPs between East Asian and European populations. Our systematic survey did not yield conclusive evidence to support the Thrifty Gene hypothesis as a possible explanation for the differences observed between East Asians and Europeans.

Thinking evolutionarily about obesity

Obesity, diabetes, and metabolic syndrome are growing worldwide health concerns, yet their causes are not fully understood. Research into the etiology of the obesity epidemic is highly influenced by our understanding of the evolutionary roots of metabolic control. For half a century, the thrifty gene hypothesis, which argues that obesity is an evolutionary adaptation for surviving periods of famine, has dominated the thinking on this topic. Obesity researchers are often not aware that there is, in fact, limited evidence to support the thrifty gene hypothesis and that alternative hypotheses have been suggested. This review presents evidence for and against the thrifty gene hypothesis and introduces readers to additional hypotheses for the evolutionary origins of the obesity epidemic. Because these alternate hypotheses imply significantly different strategies for research and clinical management of obesity, their consideration is critical to halting the spread of this epidemic.

Race, regionality and pre-diabetes in the Reasons for Geographic and Racial Differences in Stroke (REGARDS) study

OBJECTIVE

To determine the association between race, region and pre-diabetes.

METHOD

The study used 2003-2007 United States baseline data from the Reasons for Geographic and Racial Differences in Stroke (REGARDS) study for this cross-sectional analysis. Participants in this study were 45years or older at recruitment. Logistic regression was used to assess whether race and region are associated with pre-diabetes independent of demographics, socioeconomic factors and risk factors.

RESULTS

Twenty-four percent of the study participants (n=19,889) had pre-diabetes. The odds ratio (95% confidence interval) for having pre-diabetes was 1.28 (1.19-1.36) for blacks relative to whites and 1.18 (1.10-1.26) for people living in the Stroke Belt region relative to the other parts of the United States. The odds of having pre-diabetes for Stroke Belt participants changed minimally after additional adjustment for race (OR=1.20; 1.13-1.28), age and sex (OR=1.24; 1.16-1.32), socioeconomic status (OR=1.22; 1.15-1.31) and risk factors (OR=1.26; 1.17-1.35). In the adjusted model, being black was independently associated with pre-diabetes (OR=1.19; 1.10-1.28).

CONCLUSION

The prevalence of pre-diabetes was higher for both blacks and whites living in the Stroke Belt relative to living outside the Stroke Belt, and the prevalence of pre-diabetes was higher for blacks independent of region.

Colorectal cancer risk and patients' survival: influence of polymorphisms in genes somatically mutated in colorectal tumors

PURPOSE

The first two studies aiming for the high-throughput identification of the somatic mutation spectrum of colorectal cancer (CRC) tumors were published in 2006 and 2007. Using exome sequencing, they described 69 and 140 candidate cancer genes (CAN genes), respectively. We hypothesized that germline variants in these genes may influence CRC risk, similar to APC, which is causing CRC through germline and somatic mutations.

METHODS

After excluding the well-established CRC genes APC, KRAS, TP53, and ABCA1, we analyzed 35 potentially functional single-nucleotide polymorphisms (SNPs) in 10 CAN genes (OBSCN, MLL3, PKHD1, SYNE1, ERCC6, FBXW7, EPHB6/TRPV6, ELAC1/SMAD4, EPHA3, and ADAMTSL3) using KBiosciences Competitive Allele-Specific PCR™ genotyping assays. In addition to CRC risk (1,399 CRC cases, 838 controls), we also considered the influence of the SNPs on patients' survival (406 cases).

RESULTS

In spite of the fact that our in silico analyses suggested functional relevance for the studied genes and SNPs, our data did not support a strong influence of the studied germline variants on CRC risk and survival. The strongest association with CRC risk and survival was found for MLL3 (rs6464211, OR 1.50, p = 0.002, dominant model; HR 2.12, p = 0.020, recessive model). Two SNPs in EPHB6/TRPV6 (dominant model) showed marginal associations with survival (rs4987622 HR 0.58 p = 0.028 and rs6947538 HR 0.64, p = 0.036, respectively).

CONCLUSION

Although somatic mutations in the CAN genes have been related to the development and progression of various types of cancers in several next-generation sequencing or expression analyses, our study suggests that the studied potentially functional germline variants are not likely to affect CRC risk or survival.

Evolutionary perspectives on the obesity epidemic: adaptive, maladaptive, and neutral viewpoints

The prevalence of obesity in modern societies has two major contributory factors-an environmental change that has happened in historical times and a genetic predisposition that has its origins in our evolutionary history. Understanding both aspects is complex. From an evolutionary perspective, three different types of explanation have been proposed. The first is that obesity was once adaptive and enabled us to survive (or sustain fecundity) through periods of famine. People carrying so-called thrifty genes that enabled the efficient storage of energy as fat between famines would be at a selective advantage. In the modern world, however, people who have inherited these genes deposit fat in preparation for a famine that never comes, and the result is widespread obesity. The key problem with this, and any other adaptive scenario, is to understand why, if obesity was historically so advantageous, many people did not inherit these thrifty genes and in modern society are able to remain slim, despite the environmental change favoring fat storage. The second type of explanation is that obesity is not adaptive and may never even have existed in our evolutionary past, but it is favored today as a maladaptive by-product of positive selection on some other trait. An example of this type of explanation is the suggestion that obesity results from variation in brown adipose tissue thermogenesis. Finally, a third class of explanation is that most mutations in the genes that predispose us to obesity are neutral and have been drifting over evolutionary time--so-called drifty genes, leading some individuals to be obesity prone and others obesity resistant. In this article, I review the current evidence for and against these three different scenarios and conclude that the thrifty gene hypothesis is untenable but the other two ideas may provide a cogent explanation of the modern obesity phenomenon.

Revisiting the thrifty gene hypothesis via 65 loci associated with susceptibility to type 2 diabetes

We have investigated the evidence for positive selection in samples of African, European, and East Asian ancestry at 65 loci associated with susceptibility to type 2 diabetes (T2D) previously identified through genome-wide association studies. Selection early in human evolutionary history is predicted to lead to ancestral risk alleles shared between populations, whereas late selection would result in population-specific signals at derived risk alleles. By using a wide variety of tests based on the site frequency spectrum, haplotype structure, and population differentiation, we found no global signal of enrichment for positive selection when we considered all T2D risk loci collectively. However, in a locus-by-locus analysis, we found nominal evidence for positive selection at 14 of the loci. Selection favored the protective and risk alleles in similar proportions, rather than the risk alleles specifically as predicted by the thrifty gene hypothesis, and may not be related to influence on diabetes. Overall, we conclude that past positive selection has not been a powerful influence driving the prevalence of T2D risk alleles.

Insights into the genetic susceptibility to type 2 diabetes from genome-wide association studies of glycaemic traits

Over the past 8 years, the genetics of complex traits have benefited from an unprecedented advancement in the identification of common variant loci for diseases such as type 2 diabetes (T2D). The ability to undertake genome-wide association studies in large population-based samples for quantitative glycaemic traits has permitted us to explore the hypothesis that models arising from studies in non-diabetic individuals may reflect mechanisms involved in the pathogenesis of diabetes. Amongst 88 T2D risk and 72 glycaemic trait loci, only 29 are shared and show disproportionate magnitudes of phenotypic effects. Important mechanistic insights have been gained regarding the physiological role of T2D loci in disease predisposition through the elucidation of their contribution to glycaemic trait variability. Further investigation is warranted to define causal variants within these loci, including functional characterisation of associated variants, to dissect their role in disease mechanisms and to enable clinical translation.

Signatures of natural selection on genetic variants affecting complex human traits

It has recently been hypothesized that polygenic adaptation, resulting in modest allele frequency changes at many loci, could be a major mechanism behind the adaptation of complex phenotypes in human populations. Here we leverage the large number of variants that have been identified through genome-wide association (GWA) studies to comprehensively study signatures of natural selection on genetic variants associated with complex traits. Using population differentiation based methods, such as FST and phylogenetic branch length analyses, we systematically examined nearly 1300 SNPs associated with 38 complex phenotypes. Instead of detecting selection signatures at individual variants, we aimed to identify combined evidence of natural selection by aggregating signals across many trait associated SNPs. Our results have revealed some general features of polygenic selection on complex traits associated variants. First, natural selection acting on standing variants associated with complex traits is a common phenomenon. Second, characteristics of selection for different polygenic traits vary both temporarily and geographically. Third, some studied traits (e.g. height and urate level) could have been the primary targets of selection, as indicated by the significant correlation between the effect sizes and the estimated strength of selection in the trait associated variants; however, for most traits, the allele frequency changes in trait associated variants might have been driven by the selection on other correlated phenotypes. Fourth, the changes in allele frequencies as a result of selection can be highly stochastic, such that, polygenic adaptation may accelerate differentiation in allele frequencies among populations, but generally does not produce predictable directional changes. Fifth, multiple mechanisms (pleiotropy, hitchhiking, etc) may act together to govern the changes in allele frequencies of genetic variants associated with complex traits.

The protective effect of the obesity-associated rs9939609 A variant in fat mass- and obesity-associated gene on depression

Candidate gene and genome-wide association studies have not identified common variants, which are reliably associated with depression. The recent identification of obesity predisposing genes that are highly expressed in the brain raises the possibility of their genetic contribution to depression. As variation in the intron 1 of the fat mass- and obesity-associated (FTO) gene contributes to polygenic obesity, we assessed the possibility that FTO gene may contribute to depression in a cross-sectional multi-ethnic sample of 6561 depression cases and 21,932 controls selected from the EpiDREAM, INTERHEART, DeCC (depression case-control study) and Cohorte Lausannoise (CoLaus) studies. Major depression was defined according to DSM IV diagnostic criteria. Association analyses were performed under the additive genetic model. A meta-analysis of the four studies showed a significant inverse association between the obesity risk FTO rs9939609 A variant and depression (odds ratio=0.92 (0.89, 0.97), P=3 × 10(-4)) adjusted for age, sex, ethnicity/population structure and body-mass index (BMI) with no significant between-study heterogeneity (I(2)=0%, P=0.63). The FTO rs9939609 A variant was also associated with increased BMI in the four studies (β 0.30 (0.08, 0.51), P=0.0064) adjusted for age, sex and ethnicity/population structure. In conclusion, we provide the first evidence that the FTO rs9939609 A variant may be associated with a lower risk of depression independently of its effect on BMI. This study highlights the potential importance of obesity predisposing genes on depression.

Evidence of selection at insulin receptor substrate-1 gene loci

Type 2 diabetes mellitus (T2DM) is a complex disease characterized by insulin resistance and defect of insulin secretion. The worldwide prevalence of T2DM is steadily increasing. T2DM is also significantly associated with obesity, coronary artery disease (CAD), and metabolic syndrome. There is a clear difference in the prevalence of T2DM among populations, and T2DM is highly heritable. Human adaptations to environmental changes in food supply, lifestyle, and geography may have pressured the selection of genes associated with the metabolism of glucose, lipids, carbohydrates, and energy. The insulin receptor substrate-1 (IRS1) gene is considered a major T2DM gene, and common genetic variations near the IRS1 gene were found to be associated with T2DM, insulin resistance, adiposity, and CAD. Here, we aimed to find evidence of selection at the IRS1 gene loci using the HapMap population data. We investigated a 3-step test procedure-Wright's F statistics (Fst), the long-range haplotype (LRH) test, and the integrated haplotype score (iHS) test-to detect selection at the IRS1 gene loci using the HapMap population data. We observed that 1 CAD-associated SNP (rs2943634) and 1 adiposity- and insulin resistance-associated SNP (rs2943650) exhibited high Fst values. We also found selection at the IRS1 gene loci by the LRH test and the iHS test. These findings suggest evidence of selection at the IRS1 gene loci and that further studies should examine the adaptive evolution of T2DM genes.

Variation at diabetes- and obesity-associated Loci may mirror neutral patterns of human population diversity and diabetes prevalence in India

South Asian populations harbor a high degree of genetic diversity, due in part to demographic history. Two studies on genome-wide variation in Indian populations have shown that most Indian populations show varying degrees of admixture between ancestral north Indian and ancestral south Indian components. As a result of this structure, genetic variation in India appears to follow a geographic cline. Similarly, Indian populations seem to show detectable differences in diabetes and obesity prevalence between different geographic regions of the country. We tested the hypothesis that genetic variation at diabetes- and obesity-associated loci may be potentially related to different genetic ancestries. We genotyped 2977 individuals from 61 populations across India for 18 SNPs in genes implicated in T2D and obesity. We examined patterns of variation in allele frequency across different geographical gradients and considered state of origin and language affiliation. Our results show that most of the 18 SNPs show no significant correlation with latitude, the geographic cline reported in previous studies, or by language family. Exceptions include KCNQ1 with latitude and THADA and JAK1 with language, which suggests that genetic variation at previously ascertained diabetes-associated loci may only partly mirror geographic patterns of genome-wide diversity in Indian populations.

The genetics of childhood obesity and interaction with dietary macronutrients

The genes contributing to childhood obesity are categorized into three different types based on distinct genetic and phenotypic characteristics. These types of childhood obesity are represented by rare monogenic forms of syndromic or non-syndromic childhood obesity, and common polygenic childhood obesity. In some cases, genetic susceptibility to these forms of childhood obesity may result from different variations of the same gene. Although the prevalence for rare monogenic forms of childhood obesity has not increased in recent times, the prevalence of common childhood obesity has increased in the United States and developing countries throughout the world during the past few decades. A number of recent genome-wide association studies and mouse model studies have established the identification of susceptibility genes contributing to common childhood obesity. Accumulating evidence suggests that this type of childhood obesity represents a complex metabolic disease resulting from an interaction with environmental factors, including dietary macronutrients. The objective of this article is to provide a review on the origins, mechanisms, and health consequences of obesity susceptibility genes and interaction with dietary macronutrients that predispose to childhood obesity. It is proposed that increased knowledge of these obesity susceptibility genes and interaction with dietary macronutrients will provide valuable insight for individual, family, and community preventative lifestyle intervention, and eventually targeted nutritional and medicinal therapies.

Transferability and fine mapping of type 2 diabetes loci in African Americans: the Candidate Gene Association Resource Plus Study

Type 2 diabetes (T2D) disproportionally affects African Americans (AfA) but, to date, genetic variants identified from genome-wide association studies (GWAS) are primarily from European and Asian populations. We examined the single nucleotide polymorphism (SNP) and locus transferability of 40 reported T2D loci in six AfA GWAS consisting of 2,806 T2D case subjects with or without end-stage renal disease and 4,265 control subjects from the Candidate Gene Association Resource Plus Study. Our results revealed that seven index SNPs at the TCF7L2, KLF14, KCNQ1, ADCY5, CDKAL1, JAZF1, and GCKR loci were significantly associated with T2D (P < 0.05). The strongest association was observed at TCF7L2 rs7903146 (odds ratio [OR] 1.30; P = 6.86 × 10⁻⁸). Locus-wide analysis demonstrated significant associations (P(emp) < 0.05) at regional best SNPs in the TCF7L2, KLF14, and HMGA2 loci as well as suggestive signals in KCNQ1 after correction for the effective number of SNPs at each locus. Of these loci, the regional best SNPs were in differential linkage disequilibrium (LD) with the index and adjacent SNPs. Our findings suggest that some loci discovered in prior reports affect T2D susceptibility in AfA with similar effect sizes. The reduced and differential LD pattern in AfA compared with European and Asian populations may facilitate fine mapping of causal variants at loci shared across populations.