University Biology Classrooms as Spaces for Anti-racist Work: Instructor Motivations for Incorporating Race, Racism, and Racial Equity Content

Science is often portrayed as a meritocratic endeavor, but university biology programs exhibit high rates of student attrition, particularly among students of Color, despite similar interest and aptitude for science, technology, engineering, and mathematics (STEM) as White students. Culturally relevant pedagogy is associated with student persistence in STEM. One way to practice culturally relevant pedagogy in biology courses is to engage students in discussions of race, racism, or racial equity. Guidance exists to help instructors incorporate race-related topics into the biology curriculum, but the reasoning behind the decision of whether to adopt this practice is not well characterized. Understanding instructors' perceptions and experiences in implementing these topics will help identify supports and address barriers to instructor adoption. In this study, we examine university biology instructors' motivations for incorporating topics of race, racism, or racial equity in biology courses and contextual factors that influence this motivation. We found that the instructors were primarily motivated by intrinsic factors, desire to promote student learning and success, and social injustice events despite lacking external incentives. The instructors also held anti-racist perspectives when developing learning experiences for their students. How change agents can leverage these findings to promote rightful presence in biology courses is discussed.

Modeling recent positive selection using identity-by-descent segments

Recent positive selection can result in an excess of long identity-by-descent (IBD) haplotype segments overlapping a locus. The statistical methods that we propose here address three major objectives in studying selective sweeps: scanning for regions of interest, identifying possible sweeping alleles, and estimating a selection coefficient s. First, we implement a selection scan to locate regions with excess IBD rates. Second, we estimate the allele frequency and location of an unknown sweeping allele by aggregating over variants that are more abundant in an inferred outgroup with excess IBD rate versus the rest of the sample. Third, we propose an estimator for the selection coefficient and quantify uncertainty using the parametric bootstrap. Comparing against state-of-the-art methods in extensive simulations, we show that our methods are more precise at estimating s when s≥0.015. We also show that our 95% confidence intervals contain s in nearly 95% of our simulations. We apply these methods to study positive selection in European ancestry samples from the Trans-Omics for Precision Medicine project. We analyze eight loci where IBD rates are more than four standard deviations above the genome-wide median, including LCT where the maximum IBD rate is 35 standard deviations above the genome-wide median. Overall, we present robust and accurate approaches to study recent adaptive evolution without knowing the identity of the causal allele or using time series data.

HaploSweep: Detecting and Distinguishing Recent Soft and Hard Selective Sweeps through Haplotype Structure

Identifying soft selective sweeps using genomic data is a challenging yet crucial task in population genetics. In this study, we present HaploSweep, a novel method for detecting and categorizing soft and hard selective sweeps based on haplotype structure. Through simulations spanning a broad range of selection intensities, softness levels, and demographic histories, we demonstrate that HaploSweep outperforms iHS, nSL, and H12 in detecting soft sweeps. HaploSweep achieves high classification accuracy-0.9247 for CHB, 0.9484 for CEU, and 0.9829 YRI-when applied to simulations in line with the human Out-of-Africa demographic model. We also observe that the classification accuracy remains consistently robust across different demographic models. Additionally, we introduce a refined method to accurately distinguish soft shoulders adjacent to hard sweeps from soft sweeps. Application of HaploSweep to genomic data of CHB, CEU, and YRI populations from the 1000 genomes project has led to the discovery of several new genes that bear strong evidence of population-specific soft sweeps (HRNR, AMBRA1, CBFA2T2, DYNC2H1, and RANBP2 etc.), with prevalent associations to immune functions and metabolic processes. The validated performance of HaploSweep, demonstrated through both simulated and real data, underscores its potential as a valuable tool for detecting and comprehending the role of soft sweeps in adaptive evolution.

Genetic aspects of lactase deficiency in indigenous populations of Siberia

The ability to metabolize lactose in adulthood is associated with the persistence of lactase enzyme activity. In European populations, lactase persistence is determined mainly by the presence of the rs4988235-T variant in the MCM6 gene, which increases the expression of the LCT gene, encoding lactase. The highest rates of lactase persistence are characteristic of Europeans, and the lowest rates are found in East Asian populations. Analysis of published data on the distribution of the hypolactasia-associated variant rs4988235-C in the populations of Central Asia and Siberia showed that the frequency of this variant increases in the northeastern direction. The frequency of this allele is 87 % in Central Asia, 90.6 % in Southern Siberia, and 92.9 % in Northeastern Siberia. Consequently, the ability of the population to metabolize lactose decreases in the same geographical direction. The analysis of paleogenomic data has shown that the higher frequency of the rs4988235-T allele in populations of Central Asia and Southern Siberia is associated with the eastward spread of ancient populations of the Eastern European steppes, starting from the Bronze Age. The results of polymorphism analysis of exons and adjacent introns of the MCM6 and LCT genes in indigenous populations of Siberia indicate the possibility that polymorphic variants may potentially be related to lactose metabolism exist in East Asian populations. In East Asian populations, including Siberian ethnic groups, a ~26.5 thousand nucleotide pairs long region of the MCM6 gene, including a combination of the rs4988285-A, rs2070069-G, rs3087353-T, and rs2070068-A alleles, was found. The rs4988285 and rs2070069 loci are located in the enhancer region that regulates the activity of the LCT gene. Analysis of paleogenomic sequences showed that the genomes of Denisovans and Neanderthals are characterized by the above combination of alleles of the MCM6 gene. Thus, the haplotype discovered appears to be archaic. It could have been inherited from a common ancestor of modern humans, Neanderthals, and Denisovans, or it could have been acquired by hybridization with Denisovans or Neanderthals. The data obtained indicate a possible functional significance of archaic variants of the MCM6 gene.

The role of culture in the representation of probiotic foods

Functional foods, and specifically probiotics, are important products present in retail worldwide. Probiotics comprise "live microorganisms that, when administered in adequate amounts, can confer a health benefit on the host". This study aimed to investigate the effect of culture on probiotic foods social representation. A total of 818 consumers from seven countries (Argentina, Brazil, Honduras, Mauritius, Mexico, Peru, and Slovenia) participated in the study. A free word association task was performed with the inductor term "probiotic food," followed by lemmatization, categorization, and prototypical analysis of the social representation. The results indicated that the term health was common in all countries studied, as well as other positive aspects such as benefits, well-being, and functional foods. This study helped to shed light and better understand the role of culture in the social representation of probiotics.

Bone Mineral Density and the Risk of Type-2 Diabetes in Postmenopausal Women: rs4988235 Polymorphism Associated with Lactose Intolerance Effects

Dairy products, a major source of calcium, demonstrate a number of beneficial effects, not only protecting against the development of osteoporosis (OP) but also suppressing the onset of type-2 diabetes (T2DM) and improving bone mineral density (BMD). Dairy consumption is closely linked to lactose tolerance. One of the genetic factors predisposing individuals to lactose intolerance is rs4988235 polymorphism of the MCM6 gene. The aim of this reported study was to analyse the relationship between the rs4988235 variant of the MCM6 gene and bone mineral density and the risk of type-2 diabetes in women after menopause.

METHODS

The study was conducted among 607 female patients in the postmenopausal period in whom bone densitometry and vitamin-D3 levels were assayed and genotyping of the rs4988235 polymorphism of MCM6 gene was performed. The obtained results were analysed for the presence of T2DM, obesity surrogates, medical data, and past medical history.

RESULTS

The distribution of genotype frequencies was consistent with the Hardy-Weinberg equilibrium (p > 0.050). Postmenopausal women with the GG homozygote of rs4988235 polymorphism consumed significantly less calcium (dairy), which was probably related to the observed lactose intolerance. The GG homozygote of women with rs4988235 polymorphism was significantly more likely to have T2DM relative to the A allele carriers (p = 0.023). GG homozygotes had significantly lower femoral-vertebral mineral density despite the significantly more frequent supplementation with calcium preparations (p = 0.010), vitamin D (p = 0.01), and anti-osteoporotic drugs (p = 0.040). The obtained results indicate a stronger loss of femoral-neck mineral density with age in the GG homozygotes relative to the A allele carriers (p = 0.038).

CONCLUSIONS

In the population of women after menopause, the carriage of the G allele of rs4988235 polymorphism of the MCM6 gene, i.e., among the patients with lactose intolerance, significantly increased the risk of developing T2DM and the loss of BMD.

Exploration of dietary interventions to treat mitochondrial fatty acid disorders in a mouse model

Mitochondrial fatty acids synthesis (mtFAS) is a conserved metabolic pathway essential for mitochondrial respiration. The best characterized mtFAS product is the medium-chain fatty acid octanoate (C8) used as a substrate in the synthesis of lipoic acid (LA), a cofactor required by several mitochondrial enzyme complexes. In humans, mutations in the mtFAS component enoyl reductase MECR cause childhood-onset neurodegenerative disorder MEPAN. A complete deletion of Mecr in mice is embryonically lethal, while selective deletion of Mecr in cerebellar Purkinje cells causes neurodegeneration in these cells. A fundamental question in the research of mtFAS deficiency is if the defect is amenable to treatment by supplementation with known mtFAS products. Here we used the Purkinje-cell specific mtFAS deficiency neurodegeneration model mice to study if feeding the mice with a medium-chain triacylglycerol-rich formula supplemented with LA could slow down or prevent the neurodegeneration in Purkinje cell-specific Mecr KO mice. Feeding started at the age of 4 weeks and continued until the age of 9 months. The neurological status on the mice was assessed at the age of 3, 6, and 9 months with behavioral tests and the state of the Purkinje cell deterioration in the cerebellum was studied histologically. We showed that feeding the mice with medium chain triacylglycerols and LA affected fatty acid profiles in the cerebellum and plasma but did not prevent the development of neurodegeneration in these mice. Our results indicate that dietary supplementation with medium chain fatty acids and LA alone is not an efficient way to treat mtFAS disorders.

Lactase persistence in the Jordanian population: Potential effects of the Arabian Peninsula and Sahara's aridification

The single nucleotide polymorphism (SNP) -13910 C > T has proved a good predictor of the incidence of lactase persistence in Europe and South Asia. Yet, this is not the case in the Near East, although this region is a passageway between the two continents. Lactase persistence is associated with cattle breeding, which originated in the Fertile Crescent of the Near East and spread later during the Middle Neolithic throughout Europe. Here we analyzed five SNPs (-13915 T > G (rs41380347), -13910 C > T (rs4988235), -13907 C > G (rs41525747), -14009 T > G (rs869051967), and -14010 G > C (rs145946881)) in three Jordanian human groups, namely the Bedouins, Jordan valley farmers, and Jordanian urban people. The SNPs -14009 T > G and -14010 G > C were not detected in the sample, -13907 C > G was virtually non-existent, -13910 C > T showed low frequencies, and -13915 T > G exhibited salient frequencies. The estimated incidence of lactase persistence was lower in the urban population (16 %), intermediate in the Jordan Valley's farmer population (30 %), and higher among the Bedouins (62 %). In explaining our findings, we postulated climatic change brought about by the aridification episode of the Arabian Peninsula and the Sahara 4200 years ago. This climatic milestone caused the collapse of the Akkadian Empire and the Old Kingdom in Egypt. Also, it could have led to a drastic decline of cattle in the region, being replaced by the domestication of camels. Loss of traditional crops and increasing dependence on camel milk might have triggered local selective pressures, mainly associated with -13915 T > G and differentiated from the ones in Europe, associated with -13910 C > T.

Evolution: Spectral speciation

Speciation is a complex process sparked by multitudes of environmental stressors and culminating in adaptive, and perhaps novel, phenotypic traits. A new study presents evidence supporting spectral niche-partitioning in a cyanobacterial clade specializing in far-red photosynthesis.

Emerging Parameters Justifying a Revised Quality Concept for Cow Milk

Milk has become a staple food product globally. Traditionally, milk quality assessment has been primarily focused on hygiene and composition to ensure its safety for consumption and processing. However, in recent years, the concept of milk quality has expanded to encompass a broader range of factors. Consumers now also consider animal welfare, environmental impact, and the presence of additional beneficial components in milk when assessing its quality. This shifting consumer demand has led to increased attention on the overall production and sourcing practices of milk. Reflecting on this trend, this review critically explores such novel quality parameters, offering insights into how such practices meet the modern consumer's holistic expectations. The multifaceted aspects of milk quality are examined, revealing the intertwined relationship between milk safety, compositional integrity, and the additional health benefits provided by milk's bioactive properties. By embracing sustainable farming practices, dairy farmers and processors are encouraged not only to fulfill but to anticipate consumer standards for premium milk quality. This comprehensive approach to milk quality underscores the necessity of adapting dairy production to address the evolving nutritional landscape and consumption patterns.

From bowls to pots: The dairying revolution in Northwest Turkey, a view from Barcın Höyük, 6600 to 6000 BCE

Research has identified Northwest Turkey as a key region for the development of dairying in the seventh millennium BCE, yet little is known about how this practice began or evolved there. This research studies Barcın Höyük, a site located in Bursa's Yenişehir Valley, which ranges chronologically from 6600 BCE, when the first evidence of settled life appears in the Marmara Region, to 6000 BCE, when Neolithic habitation at the site ceases. Using pottery sherds diagnostic by vessel category and type, this paper aims at identifying which ones may have been primarily used to store, process, or consume dairy products. Organic residue analysis of selected samples helped address the process of adoption and intensification of milk processing in this region over time. The lipid residue data discussed in this paper derive from 143 isotopic results subsampled from 173 organic residues obtained from 805 Neolithic potsherds and suggest that bowls and four-lugged pots may have been preferred containers for processing milk. The discovery of abundant milk residues even among the earliest ceramics indicates that the pioneer farmers arrived in the region already with the knowhow of dairying and milk processing. In fact, these skills and the reliance on secondary products may have given them one of the necessary tools to successfully venture into the unfarmed lands of Northwest Anatolia in the first place.

Prebiotic Strategies to Manage Lactose Intolerance Symptoms

Lactose intolerance, which affects about 65-75% of the world's population, is caused by a genetic post-weaning deficiency of lactase, the enzyme required to digest the milk sugar lactose, called lactase non-persistence. Symptoms of lactose intolerance include abdominal pain, bloating and diarrhea. Genetic variations, namely lactase persistence, allow some individuals to metabolize lactose effectively post-weaning, a trait thought to be an evolutionary adaptation to dairy consumption. Although lactase non-persistence cannot be altered by diet, prebiotic strategies, including the consumption of galactooligosaccharides (GOSs) and possibly low levels of lactose itself, may shift the microbiome and mitigate symptoms of lactose consumption. This review discusses the etiology of lactose intolerance and the efficacy of prebiotic approaches like GOSs and low-dose lactose in symptom management.

EVALUATION OF AGREEMENT BETWEEN C/T-13910 POLYMORPHISM GENOTYPING RESULTS AND LACTOSE TOLERANCE TEST RESULTS: A RETROSPECTIVE POPULATION-BASED STUDY IN BRAZIL

BACKGROUND

Lactose tolerant test (LTT) is the most broadly used diagnostic test for lactose intolerance in Brazil, is an indirect, minimally invasive and a low-cost test that is widely available in primary care and useful in clinical practice. The C/T-13910 polymorphism in lactase persistence has been well characterized in Caucasian populations, but there are no studies evaluating the concordance between C/T-13910 polymorphism genotyping results and LTT results in Brazil, where the population is highly mixed.

OBJECTIVE

We aimed to evaluate agreement between presence of C/T-13910 polymorphism genotyping and malabsorption in LTT results.

METHODS

This is a retrospective analysis of a Brazilian population whose data were collected from a single laboratory database present in several Brazilian states. Results of individuals who underwent both genetic testing for lactose intolerance (C/T-13910 polymorphism genotyping) and an LTT from April 2016 until February 2019 were analysed to evaluate agreement between tests. Groups were classified according to age (<10-year-old (yo), 10-17 yo, ≥18 yo groups) and state of residence (São Paulo or Rio Grande do Sul). Results: Among the 404 patients evaluated, there was agreement between the genotyping and LTT results in 325 (80.4%) patients and discordance in 79 (19.6%) patients (k=0.42 -moderate agreement). Regarding the genotype, 47 patients with genotype C/C (lactase nonpersistence) had normal LTT results, and 32 with genotype C/T or T/T (indicating lactase persistence) had abnormal LTT results. Neither age nor state of residence (Rio Grande do Sul or São Paulo) affected the agreement between test results.

CONCLUSION

Considering the moderate agreement between C/T-13910 polymorphism genotyping and LTT results (κ=0.42) in the Brazilian population, we hypothesize that an analysis of other polymorphisms could be a strategy to improve the agreement between genotyping and established tests and suggest that additional studies should focus on exploring this approach.

Modifying Dietary Sodium and Potassium Intake: An End to the 'Salt Wars'?

Excessive salt intake raises blood pressure, but the implications of this observation for human health have remained contentious. It has also been recognized for many years that potassium intake may mitigate the effects of salt intake on blood pressure and possibly on outcomes such as stroke. Recent large randomized intervention trials have provided strong support for the benefits of replacing salt (NaCl) with salt substitute (75% NaCl, 25% KCl) on hard outcomes, including stroke. During the same period of time, major advances have been made in understanding how the body senses and tastes salt, and how these sensations drive intake. Additionally, new insights into the complex interactions between systems that control sodium and potassium excretion by the kidneys, and the brain have highlighted the existence of a potassium switch in the kidney distal nephron. This switch seems to contribute importantly to the blood pressure-lowering effects of potassium intake. In recognition of these evolving data, the United States Food and Drug Administration is moving to permit potassium-containing salt substitutes in food manufacturing. Given that previous attempts to reduce salt consumption have not been successful, this new approach has a chance of improving health and ending the 'Salt Wars'.

Predicting Functional Consequences of Recent Natural Selection in Britain

Ancient DNA can directly reveal the contribution of natural selection to human genomic variation. However, while the analysis of ancient DNA has been successful at identifying genomic signals of selection, inferring the phenotypic consequences of that selection has been more difficult. Most trait-associated variants are noncoding, so we expect that a large proportion of the phenotypic effects of selection will also act through noncoding variation. Since we cannot measure gene expression directly in ancient individuals, we used an approach (Joint-Tissue Imputation [JTI]) developed to predict gene expression from genotype data. We tested for changes in the predicted expression of 17,384 protein coding genes over a time transect of 4,500 years using 91 present-day and 616 ancient individuals from Britain. We identified 28 genes at seven genomic loci with significant (false discovery rate [FDR] < 0.05) changes in predicted expression levels in this time period. We compared the results from our transcriptome-wide scan to a genome-wide scan based on estimating per-single nucleotide polymorphism (SNP) selection coefficients from time series data. At five previously identified loci, our approach allowed us to highlight small numbers of genes with evidence for significant shifts in expression from peaks that in some cases span tens of genes. At two novel loci (SLC44A5 and NUP85), we identify selection on gene expression not captured by scans based on genomic signatures of selection. Finally, we show how classical selection statistics (iHS and SDS) can be combined with JTI models to incorporate functional information into scans that use present-day data alone. These results demonstrate the potential of this type of information to explore both the causes and consequences of natural selection.

Human adaptations to diet: Biological and cultural coevolution

Modern humans evolved in Africa some 200,000 years ago, and since then, human populations have expanded and diversified to occupy a broad range of habitats and use different subsistence modes. This has resulted in different adaptations, such as differential responses to diseases and different abilities to digest or tolerate certain foods. The shift from a subsistence strategy based on hunting and gathering during the Palaeolithic to a lifestyle based on the consumption of domesticated animals and plants in the Neolithic can be considered one of the most important dietary transitions of Homo sapiens. In this text, we review four examples of gene-culture coevolution: (i) the persistence of the enzyme lactase after weaning, which allows the digestion of milk in adulthood, related to the emergence of dairy farming during the Neolithic; (ii) the population differences in alcohol susceptibility, in particular the ethanol intolerance of Asian populations due to the increased accumulation of the toxic acetaldehyde, related to the spread of rice domestication; (iii) the maintenance of gluten intolerance (celiac disease) with the subsequent reduced fitness of its sufferers, related to the emergence of agriculture and (iv) the considerable variation in the biosynthetic pathway of long-chain polyunsaturated fatty acids in native populations with extreme diets.

TRAILS: Tree reconstruction of ancestry using incomplete lineage sorting

Genome-wide genealogies of multiple species carry detailed information about demographic and selection processes on individual branches of the phylogeny. Here, we introduce TRAILS, a hidden Markov model that accurately infers time-resolved population genetics parameters, such as ancestral effective population sizes and speciation times, for ancestral branches using a multi-species alignment of three species and an outgroup. TRAILS leverages the information contained in incomplete lineage sorting fragments by modelling genealogies along the genome as rooted three-leaved trees, each with a topology and two coalescent events happening in discretized time intervals within the phylogeny. Posterior decoding of the hidden Markov model can be used to infer the ancestral recombination graph for the alignment and details on demographic changes within a branch. Since TRAILS performs posterior decoding at the base-pair level, genome-wide scans based on the posterior probabilities can be devised to detect deviations from neutrality. Using TRAILS on a human-chimp-gorilla-orangutan alignment, we recover speciation parameters and extract information about the topology and coalescent times at high resolution.

A Genetic Lab-on-Phone Test for Point-of-Care Diagnostic of Lactose Intolerance near Patient and in less than 90 Minutes

BACKGROUND

The -13910 C/T single nucleotide polymorphism located within the MCM6 gene, an enhancer region located upstream of the lactase-phlorizin hydrolase gene, is associated with lactase persistence/non-persistence traits among the Caucasian population. The performance of a new point-of-care CE-IVD (In Vitro Diagnostic) marked isothermal lab-on-phone lactose intolerance assay, using crude samples, was assessed in comparison with Sanger sequencing using purified DNA, as reference method.

METHODS

The study was conducted following a non-probability sampling using direct buccal swab (n = 63) and capillary blood (n = 43) clinical samples from a total of 63 volunteers. A 3 × 3 confusion matrix/contingency table was used to evaluate the performance of the isothermal lab-on-phone lactose intolerance assay.

RESULTS

The isothermal lab-on-phone lactose intolerance assay successfully detected the -13910 C/T variant with a limit of detection of 5 cells/assay and demonstrated an overall accuracy of 98.41% (95% CI, 91.47%-99.96%) for buccal swab samples and 100% (95% CI, 91.19%-100%) for capillary blood, taking just 90 min from sample to result, with only 2 min hands-on.

CONCLUSIONS

The lab-on-phone pocket-sized assay displayed good performance when using direct buccal swab and capillary blood samples, enabling a low-cost, real-time, and accurate genotyping of the -13910 C/T region for the rapid diagnosis of primary lactose intolerance at point-of-care, which enables a prompt implementation of appropriate diet habits and/or intolerance therapies. To our knowledge, this is the first point-of-care genetic test for lactose intolerance to be made available on the market.

The selection landscape and genetic legacy of ancient Eurasians

The Holocene (beginning around 12,000 years ago) encompassed some of the most significant changes in human evolution, with far-reaching consequences for the dietary, physical and mental health of present-day populations. Using a dataset of more than 1,600 imputed ancient genomes1, we modelled the selection landscape during the transition from hunting and gathering, to farming and pastoralism across West Eurasia. We identify key selection signals related to metabolism, including that selection at the FADS cluster began earlier than previously reported and that selection near the LCT locus predates the emergence of the lactase persistence allele by thousands of years. We also find strong selection in the HLA region, possibly due to increased exposure to pathogens during the Bronze Age. Using ancient individuals to infer local ancestry tracts in over 400,000 samples from the UK Biobank, we identify widespread differences in the distribution of Mesolithic, Neolithic and Bronze Age ancestries across Eurasia. By calculating ancestry-specific polygenic risk scores, we show that height differences between Northern and Southern Europe are associated with differential Steppe ancestry, rather than selection, and that risk alleles for mood-related phenotypes are enriched for Neolithic farmer ancestry, whereas risk alleles for diabetes and Alzheimer's disease are enriched for Western hunter-gatherer ancestry. Our results indicate that ancient selection and migration were large contributors to the distribution of phenotypic diversity in present-day Europeans.

Variant of the lactase LCT gene explains association between milk intake and incident type 2 diabetes

Cow's milk is frequently included in the human diet, but the relationship between milk intake and type 2 diabetes (T2D) remains controversial. Here, using data from the Hispanic Community Health Study/Study of Latinos, we show that in both sexes, higher milk intake is associated with lower risk of T2D in lactase non-persistent (LNP) individuals (determined by a variant of the lactase LCT gene, single nucleotide polymorphism rs4988235 ) but not in lactase persistent individuals. We validate this finding in the UK Biobank. Further analyses reveal that among LNP individuals, higher milk intake is associated with alterations in gut microbiota (for example, enriched Bifidobacterium and reduced Prevotella) and circulating metabolites (for example, increased indolepropionate and reduced branched-chain amino acid metabolites). Many of these metabolites are related to the identified milk-associated bacteria and partially mediate the association between milk intake and T2D in LNP individuals. Our study demonstrates a protective association between milk intake and T2D among LNP individuals and a potential involvement of gut microbiota and blood metabolites in this association.

Predicting functional consequences of recent natural selection in Britain

Ancient DNA can directly reveal the contribution of natural selection to human genomic variation. However, while the analysis of ancient DNA has been successful at identifying genomic signals of selection, inferring the phenotypic consequences of that selection has been more difficult. Most trait-associated variants are non-coding, so we expect that a large proportion of the phenotypic effects of selection will also act through non-coding variation. Since we cannot measure gene expression directly in ancient individuals, we used an approach (Joint-Tissue Imputation; JTI) developed to predict gene expression from genotype data. We tested for changes in the predicted expression of 17,384 protein coding genes over a time transect of 4500 years using 91 present-day and 616 ancient individuals from Britain. We identified 28 genes at seven genomic loci with significant (FDR < 0.05) changes in predicted expression levels in this time period. We compared the results from our transcriptome-wide scan to a genome-wide scan based on estimating per-SNP selection coefficients from time series data. At five previously identified loci, our approach allowed us to highlight small numbers of genes with evidence for significant shifts in expression from peaks that in some cases span tens of genes. At two novel loci (SLC44A5 and NUP85), we identify selection on gene expression not captured by scans based on genomic signatures of selection. Finally we show how classical selection statistics (iHS and SDS) can be combined with JTI models to incorporate functional information into scans that use present-day data alone. These results demonstrate the potential of this type of information to explore both the causes and consequences of natural selection.

Genetic and cultural adaptations underlie the establishment of dairy pastoralism in the Tibetan Plateau

BACKGROUND

Domestication and introduction of dairy animals facilitated the permanent human occupation of the Tibetan Plateau. Yet the history of dairy pastoralism in the Tibetan Plateau remains poorly understood. Little is known how Tibetans adapted to milk and dairy products.

RESULTS

We integrated archeological evidence and genetic analysis to show the picture that the dairy ruminants, together with dogs, were introduced from West Eurasia into the Tibetan Plateau since ~ 3600 years ago. The genetic admixture between the exotic and indigenous dogs enriched the candidate lactase persistence (LP) allele 10974A > G of West Eurasian origin in Tibetan dogs. In vitro experiments demonstrate that - 13838G > A functions as a LP allele in Tibetans. Unlike multiple LP alleles presenting selective signatures in West Eurasians and South Asians, the de novo origin of Tibetan-specific LP allele - 13838G > A with low frequency (~ 6-7%) and absence of selection corresponds - 13910C > T in pastoralists across eastern Eurasia steppe.

CONCLUSIONS

Results depict a novel scenario of genetic and cultural adaptations to diet and expand current understanding of the establishment of dairy pastoralism in the Tibetan Plateau.

Tensor Decomposition-based Feature Extraction and Classification to Detect Natural Selection from Genomic Data

Inferences of adaptive events are important for learning about traits, such as human digestion of lactose after infancy and the rapid spread of viral variants. Early efforts toward identifying footprints of natural selection from genomic data involved development of summary statistic and likelihood methods. However, such techniques are grounded in simple patterns or theoretical models that limit the complexity of settings they can explore. Due to the renaissance in artificial intelligence, machine learning methods have taken center stage in recent efforts to detect natural selection, with strategies such as convolutional neural networks applied to images of haplotypes. Yet, limitations of such techniques include estimation of large numbers of model parameters under nonconvex settings and feature identification without regard to location within an image. An alternative approach is to use tensor decomposition to extract features from multidimensional data although preserving the latent structure of the data, and to feed these features to machine learning models. Here, we adopt this framework and present a novel approach termed T-REx, which extracts features from images of haplotypes across sampled individuals using tensor decomposition, and then makes predictions from these features using classical machine learning methods. As a proof of concept, we explore the performance of T-REx on simulated neutral and selective sweep scenarios and find that it has high power and accuracy to discriminate sweeps from neutrality, robustness to common technical hurdles, and easy visualization of feature importance. Therefore, T-REx is a powerful addition to the toolkit for detecting adaptive processes from genomic data.

Different types of milk consumption and the risk of dementia: Analysis from a large-scale cohort study

BACKGROUND & AIMS

Previous studies have investigated whether milk consumption has a role in preventing the development of cognitive impairment, but the results were inconsistent. Importantly, most of them have disregarded the role of different types of milk. This study aimed to examine the associations between different types of milk consumption and the risk of dementia.

METHODS

In this large-scale cohort study, participants without cognitive impairment at baseline were included from the UK Biobank. The type of milk mainly used was self-reported at baseline, including full-cream milk, skimmed-milk, soy milk, other milk, and no milk. The primary outcome was all-cause dementia. Secondary outcomes included Alzheimer's disease and vascular dementia.

RESULTS

Of the 307,271 participants included in the study (mean age 56.3 [SD 8.1] years), 3789 (1.2%) incident all-cause dementia cases were observed over a median follow-up of 12.3 years. After adjustment for potential confounders, only soy milk consumers had a statistically significantly lower risk of all-cause dementia compared with no milk consumers (hazard ratio [HR], 0.69; 95% confidence interval [CI], 0.54 to 0.90). When compared with soy milk non-consumers consisting of full-cream milk, skimmed-milk, and other milk consumers, soy milk consumers still showed a lower risk of all-cause dementia (HR, 0.76; 95% CI, 0.63 to 0.92), and there was no significant interaction with genetic risk for dementia (P for interaction = 0.15). Soy milk consumers showed a lower risk of Alzheimer's disease (HR, 0.70; 95% CI, 0.51 to 0.94; P = 0.02), while the association was not significant for vascular dementia (HR, 0.72; 95% CI, 0.47 to 1.12; P = 0.14).

CONCLUSIONS

The main consumption of soy milk was associated with a lower risk of dementia, particularly non-vascular dementia. Additional studies are needed to investigate how this association varies with the dose or frequency of the consumption of soy milk and to examine the generalizability of these findings in different populations.

Milk Transmission of Mammalian Retroviruses

The transmission of viruses from one host to another typically occurs through horizontal or vertical pathways. The horizontal pathways include transmission amongst individuals, usually through bodily fluids or excretions, while vertical transmission transpires from mother to their offspring, either during pregnancy, childbirth, or breastfeeding. While there are more than 200 human pathogenic viruses to date, only a small number of them are known to be transmitted via breast milk, including cytomegalovirus (CMV), human immunodeficiency virus type 1 (HIV-1), and human T cell lymphotropic virus type 1 (HTLV-1), the latter two belonging to the family Retroviridae. Breast milk transmission is a common characteristic among mammalian retroviruses, but there is a lack of reports summarizing our knowledge regarding this route of transmission of mammalian retroviruses. Here, we provide an overview of the transmission of mammalian exogenous retroviruses with a focus on Orthoretrovirinae, and we highlight whether they have been described or suspected to be transmitted through breast milk, covering various species. We also elaborate on the production and composition of breast milk and discuss potential entry sites of exogenous mammalian retroviruses during oral transmission.

Uncovering Footprints of Natural Selection Through Spectral Analysis of Genomic Summary Statistics

Natural selection leaves a spatial pattern along the genome, with a haplotype distribution distortion near the selected locus that fades with distance. Evaluating the spatial signal of a population-genetic summary statistic across the genome allows for patterns of natural selection to be distinguished from neutrality. Considering the genomic spatial distribution of multiple summary statistics is expected to aid in uncovering subtle signatures of selection. In recent years, numerous methods have been devised that consider genomic spatial distributions across summary statistics, utilizing both classical machine learning and deep learning architectures. However, better predictions may be attainable by improving the way in which features are extracted from these summary statistics. We apply wavelet transform, multitaper spectral analysis, and S-transform to summary statistic arrays to achieve this goal. Each analysis method converts one-dimensional summary statistic arrays to two-dimensional images of spectral analysis, allowing simultaneous temporal and spectral assessment. We feed these images into convolutional neural networks and consider combining models using ensemble stacking. Our modeling framework achieves high accuracy and power across a diverse set of evolutionary settings, including population size changes and test sets of varying sweep strength, softness, and timing. A scan of central European whole-genome sequences recapitulated well-established sweep candidates and predicted novel cancer-associated genes as sweeps with high support. Given that this modeling framework is also robust to missing genomic segments, we believe that it will represent a welcome addition to the population-genomic toolkit for learning about adaptive processes from genomic data.

A Comprehensive Look at the -13910 C>T LCT Gene Polymorphism as a Molecular Marker for Vitamin D and Calcium Levels in Young Adults in Central and Eastern Europe: A Preliminary Study

Intolerance to dairy products resulting from the abnormal digestion of milk sugar (lactose) is a common cause of human gastrointestinal disorders. The aim of this study was to show that the -13910 C>T LCT gene polymorphism, together with genotypes of selected VDR gene polymorphisms and diet and nutritional status parameters, can impact the prevalence of vitamin D and calcium deficiency in young adults. This study was conducted on a group of 63 people, which comprised 21 individuals with primary adult lactase deficiency, and a control group of 42 individuals with no hypolactasia. The LCT and VDR gene genotypes were assessed using PCR restriction fragment length polymorphism (PCR-RFLP) analysis. A validated HPLC method was used to determine serum concentrations of 25(OH)D₂ and 25(OH)D₃. Atomic absorption spectrometry was used to determine calcium levels. Their diets (self-reported 7-day estimated food record), estimated calcium intakes based on the ADOS-Ca questionnaire and basic anthropometric parameters were assessed. The CC genotype associated with hypolactasia was found in 33.3% of the subjects. The presence of the CC variant of the LCT gene polymorphism in the study group of young Polish adults was found to be associated with significantly lower milk (134.7 ± 66.7 g/d vs. 342.5 ± 176 g/d; p = 0.012) and dairy product consumption (78.50 ± 36.2 g/d vs. 216.3 ± 102 g/d; p = 0.008) compared with lactase persistence. At the same time, people with adult-type primary intolerance were found to have statistically significant lower serum levels of vitamin D and calcium (p < 0.05). There was a higher chance of vitamin D and calcium deficiency and a lower intake in the group exhibiting lactase non-persistence (OR > 1). The AA variant of the VDR gene's BsmI polymorphism present in people with hypolactasia may further contribute to an increased risk of vitamin D deficiency. Exclusion of lactose from the diet, combined with impaired vitamin D metabolism, may also lead to inhibited calcium absorption by the body. Further research should be carried out on a larger group of subjects to clarify the relationship between lactase activity and vitamin D and calcium levels in young adults.

Lactase deficiency in Russia: multiethnic genetic study

BACKGROUND

Lactase persistence-the ability to digest lactose through adulthood-is closely related to evolutionary adaptations and has affected many populations since the beginning of cattle breeding. Nevertheless, the contrast initial phenotype, lactase non-persistence or adult lactase deficiency, is still observed in large numbers of people worldwide.

METHODS

We performed a multiethnic genetic study of lactase deficiency on 24,439 people, the largest in Russia to date. The percent of each population group was estimated according to the local ancestry inference results. Additionally, we calculated frequencies of rs4988235 GG genotype in Russian regions using the information of current location and birthplace data from the client's questionnaire.

RESULTS

The attained results show that among all studied population groups, the frequency of GG genotype in rs4988235 is higher than the average in the European populations. In particular, the prevalence of lactase deficiency genotype in the East Slavs group was 42.8% (95% CI: 42.1-43.4%). We also investigated the regional prevalence of lactase deficiency based on the current place of residence.

CONCLUSIONS

Our study emphasizes the significance of genetic testing for diagnostics, i.e., specifically for lactose intolerance parameter, as well as the scale of the problem of lactase deficiency in Russia which needs to be addressed by the healthcare and food sectors.

Food System Transformation and Gut Microbiota Transition: Evidence on Advancing Obesity, Cardiovascular Diseases, and Cancers-A Narrative Review

Food, a vital component of our daily life, is fundamental to our health and well-being, and the knowledge and practices relating to food have been passed down from countless generations of ancestors. Systems may be used to describe this extremely extensive and varied body of agricultural and gastronomic knowledge that has been gathered via evolutionary processes. The gut microbiota also underwent changes as the food system did, and these alterations had a variety of effects on human health. In recent decades, the gut microbiome has gained attention due to its health benefits as well as its pathological effects on human health. Many studies have shown that a person's gut microbiota partially determines the nutritional value of food and that diet, in turn, shapes both the microbiota and the microbiome. The current narrative review aims to explain how changes in the food system over time affect the makeup and evolution of the gut microbiota, advancing obesity, cardiovascular disease (CVD), and cancer. After a brief discussion of the food system's variety and the gut microbiota's functions, we concentrate on the relationship between the evolution of food system transformation and gut microbiota system transition linked to the increase of non-communicable diseases (NCDs). Finally, we also describe sustainable food system transformation strategies to ensure healthy microbiota composition recovery and maintain the host gut barrier and immune functions to reverse advancing NCDs.

Evolutionary Genetics and Admixture in African Populations

As the ancestral homeland of our species, Africa contains elevated levels of genetic diversity and substantial population structure. Importantly, African genomes are heterogeneous: They contain mixtures of multiple ancestries, each of which have experienced different evolutionary histories. In this review, we view population genetics through the lens of admixture, highlighting how multiple demographic events have shaped African genomes. Each of these historical vignettes paints a recurring picture of population divergence followed by secondary contact. First, we give a brief overview of genetic variation in Africa and examine deep population structure within Africa, including the evidence of ancient introgression from archaic "ghost" populations. Second, we describe the genetic legacies of admixture events that have occurred during the past 10,000 years. This includes gene flow between different click-speaking Khoe-San populations, the stepwise spread of pastoralism from eastern to southern Africa, multiple migrations of Bantu speakers across the continent, as well as admixture from the Middle East and Europe into the Sahel region and North Africa. Furthermore, the genomic signatures of more recent admixture can be found in the Cape Peninsula and throughout the African diaspora. Third, we highlight how natural selection has shaped patterns of genetic variation across the continent, noting that gene flow provides a potent source of adaptive variation and that selective pressures vary across Africa. Finally, we explore the biomedical implications of population structure in Africa on health and disease and call for more ethically conducted studies of genetic variation in Africa.

Tensor decomposition based feature extraction and classification to detect natural selection from genomic data

Inferences of adaptive events are important for learning about traits, such as human digestion of lactose after infancy and the rapid spread of viral variants. Early efforts toward identifying footprints of natural selection from genomic data involved development of summary statistic and likelihood methods. However, such techniques are grounded in simple patterns or theoretical models that limit the complexity of settings they can explore. Due to the renaissance in artificial intelligence, machine learning methods have taken center stage in recent efforts to detect natural selection, with strategies such as convolutional neural networks applied to images of haplotypes. Yet, limitations of such techniques include estimation of large numbers of model parameters under non-convex settings and feature identification without regard to location within an image. An alternative approach is to use tensor decomposition to extract features from multidimensional data while preserving the latent structure of the data, and to feed these features to machine learning models. Here, we adopt this framework and present a novel approach termed T-REx , which extracts features from images of haplotypes across sampled individuals using tensor decomposition, and then makes predictions from these features using classical machine learning methods. As a proof of concept, we explore the performance of T-REx on simulated neutral and selective sweep scenarios and find that it has high power and accuracy to discriminate sweeps from neutrality, robustness to common technical hurdles, and easy visualization of feature importance. Therefore, T-REx is a powerful addition to the toolkit for detecting adaptive processes from genomic data.

Uncovering the gastrointestinal passage, intestinal epithelial cellular uptake and AGO2 loading of milk miRNAs in neonates using xenomiRs as tracers

BACKGROUND

Human breast milk has a high microRNA (miRNA) content. It remains unknown whether and how milk miRNAs might affect intestinal gene regulation and homeostasis of the developing microbiome after initiation of enteral nutrition. However, this requires that relevant milk miRNA amounts survive gastrointestinal passage, are taken up by cells, and become available to the RNA interference (RNAi) machinery. It seems important to dissect the fate of these miRNAs after oral ingestion and gastrointestinal passage.

OBJECTIVE

Our goal was to analyze the potential transmissibility of milk miRNAs via the gastrointestinal system in neonate humans and a porcine model in vivo to contribute to the discussion whether milk miRNAs could influence gene regulation in neonates and thus might vertically transmit developmental relevant signals.

DESIGN

We performed cross-species profiling of miRNAs via deep-sequencing and utilized dietary xenobiotic taxon-specific milk miRNA (xenomiRs) as tracers in human and porcine neonates, followed by functional studies in primary human fetal intestinal epithelial cells (HIEC-6) using Ad5-mediated miRNA-gene transfer.

RESULTS

Mammals share many milk miRNAs yet exhibit taxon-specific miRNA fingerprints. We traced bovine-specific miRNAs from formula-nutrition in human preterm stool and 9 days after onset of enteral feeding in intestinal cells of preterm piglets. Thereafter, several xenomiRs accumulated in the intestinal cells. Moreover, few hours after introducing enteral feeding in preterm piglets with supplemented reporter miRNAs (cel-miR-39-5p/-3p), we observed their enrichment in blood serum and in AGO2-immunocomplexes from intestinal biopsies.

CONCLUSIONS

Milk-derived miRNAs survived gastrointestinal passage in human and porcine neonates. Bovine-specific miRNAs accumulated in intestinal cells of preterm piglets after enteral feeding with bovine colostrum/formula. In piglets, colostrum supplementation with cel-miR-39-5p/-3p resulted in increased blood levels of cel-miR-39-3p and argonaute RISC catalytic component 2 (AGO2) loading in intestinal cells. This suggests the possibility of vertical transmission of miRNA signaling from milk through the neonatal digestive tract.

A Population Genetic Perspective on Subsistence Systems in the Sahel/Savannah Belt of Africa and the Historical Role of Pastoralism

This review focuses on the Sahel/Savannah belt, a large region of Africa where two alternative subsistence systems (pastoralism and agriculture), nowadays, interact. It is a long-standing question whether the pastoralists became isolated here from other populations after cattle began to spread into Africa (~8 thousand years ago, kya) or, rather, began to merge with other populations, such as agropastoralists, after the domestication of sorghum and pearl millet (~5 kya) and with the subsequent spread of agriculture. If we look at lactase persistence, a trait closely associated with pastoral lifestyle, we see that its variants in current pastoralists distinguish them from their farmer neighbours. Most other (mostly neutral) genetic polymorphisms do not, however, indicate such clear differentiation between these groups; they suggest a common origin and/or an extensive gene flow. Genetic affinity and ecological symbiosis between the two subsistence systems can help us better understand the population history of this African region. In this review, we show that genomic datasets of modern Sahel/Savannah belt populations properly collected in local populations can complement the still insufficient archaeological research of this region, especially when dealing with the prehistory of mobile populations with perishable material culture and therefore precarious archaeological visibility.

Domestication and microbiome succession may drive pathogen spillover

Emerging infectious diseases have posed growing medical, social and economic threats to humanity. The biological background of pathogen spillover or host switch, however, still has to be clarified. Disease ecology finds pathogen spillovers frequently but struggles to explain at the molecular level. Contrarily, molecular biological traits of host-pathogen relationships with specific molecular binding mechanisms predict few spillovers. Here we aim to provide a synthetic explanation by arguing that domestication, horizontal gene transfer even between superkingdoms as well as gradual exchange of microbiome (microbiome succession) are essential in the whole scenario. We present a new perspective at the molecular level which can explain the observations of frequent pathogen spillover events at the ecological level. This proposed rationale is described in detail, along with supporting evidence from the peer-reviewed literature and suggestions for testing hypothesis validity. We also highlight the importance of systematic monitoring of virulence genes across taxonomical categories and in the whole biosphere as it helps prevent future epidemics and pandemics. We conclude that that the processes of domestication, horizontal gene transfer and microbial succession might be important mechanisms behind the many spillover events driven and accelerated by climate change, biodiversity loss and globalization.

Nutrigenomics in the context of evolution

Nutrigenomics describes the interaction between nutrients and our genome. Since the origin of our species most of these nutrient-gene communication pathways have not changed. However, our genome experienced over the past 50,000 years a number of evolutionary pressures, which are based on the migration to new environments concerning geography and climate, the transition from hunter-gatherers to farmers including the zoonotic transfer of many pathogenic microbes and the rather recent change of societies to a preferentially sedentary lifestyle and the dominance of Western diet. Human populations responded to these challenges not only by specific anthropometric adaptations, such as skin color and body stature, but also through diversity in dietary intake and different resistance to complex diseases like the metabolic syndrome, cancer and immune disorders. The genetic basis of this adaptation process has been investigated by whole genome genotyping and sequencing including that of DNA extracted from ancient bones. In addition to genomic changes, also the programming of epigenomes in pre- and postnatal phases of life has an important contribution to the response to environmental changes. Thus, insight into the variation of our (epi)genome in the context of our individual's risk for developing complex diseases, helps to understand the evolutionary basis how and why we become ill. This review will discuss the relation of diet, modern environment and our (epi)genome including aspects of redox biology. This has numerous implications for the interpretation of the risks for disease and their prevention.

Genome-wide allele and haplotype-sharing patterns suggested one unique Hmong-Mein-related lineage and biological adaptation history in Southwest China

BACKGROUND

Fine-scale genetic structure of ethnolinguistically diverse Chinese populations can fill the gap in the missing diversity and evolutionary landscape of East Asians, particularly for anthropologically informed Chinese minorities. Hmong-Mien (HM) people were one of the most significant indigenous populations in South China and Southeast Asia, which were suggested to be the descendants of the ancient Yangtze rice farmers based on linguistic and archeological evidence. However, their deep population history and biological adaptative features remained to be fully characterized.

OBJECTIVES

To explore the evolutionary and adaptive characteristics of the Miao people, we genotyped genome-wide SNP data in Guizhou HM-speaking populations and merged it with modern and ancient reference populations via a comprehensive population genetic analysis and evolutionary admixture modeling.

RESULTS

The overall genetic admixture landscape of Guizhou Miao showed genetic differentiation between them and other linguistically diverse Guizhou populations. Admixture models further confirmed that Miao people derived their primary ancestry from geographically close Guangxi Gaohuahua people. The estimated identity by descent and effective population size confirmed a plausible population bottleneck, contributing to their unique genetic diversity and population structure patterns. We finally identified several natural selection candidate genes associated with several biological pathways.

CONCLUSIONS

Guizhou Miao possessed a specific genetic structure and harbored a close genetic relationship with geographically close southern Chinese indigenous populations and Guangxi historical people. Miao people derived their major ancestry from geographically close Guangxi Gaohuahua people and experienced a plausible population bottleneck which contributed to the unique pattern of their genetic diversity and structure. Future ancient DNA from Shijiahe and Qujialing will provide new insights into the origin of the Miao people.

Polygenic adaptation dynamics in large, finite populations

Although many phenotypic traits are determined by a large number of genetic variants, how a polygenic trait adapts in response to a change in the environment is not completely understood. In the framework of diffusion theory, we study the steady state and the adaptation dynamics of a large but finite population evolving under stabilizing selection and symmetric mutations when selection and mutation are moderately large. We find that in the stationary state, the allele frequency distribution at a locus is unimodal if its effect size is below a threshold effect and bimodal otherwise; these results are the stochastic analog of the deterministic ones where the stable allele frequency becomes bistable when the effect size exceeds a threshold. It is known that following a sudden shift in the phenotypic optimum, in an infinitely large population, selective sweeps at a large-effect locus are prevented and adaptation proceeds exclusively via subtle changes in the allele frequency; in contrast, we find that the chance of sweep is substantially enhanced in large, finite populations and the allele frequency at a large-effect locus can reach a high frequency at short times even for small shifts in the phenotypic optimum.

ABO blood group antigens and differential glycan expression: Perspective on the evolution of common human enzyme deficiencies

Enzymes catalyze biochemical reactions and play critical roles in human health and disease. Enzyme variants and deficiencies can lead to variable expression of glycans, which can affect physiology, influence predilection for disease, and/or directly contribute to disease pathogenesis. Although certain well-characterized enzyme deficiencies result in overt disease, some of the most common enzyme deficiencies in humans form the basis of blood groups. These carbohydrate blood groups impact fundamental areas of clinical medicine, including the risk of infection and severity of infectious disease, bleeding risk, transfusion medicine, and tissue/organ transplantation. In this review, we examine the enzymes responsible for carbohydrate-based blood group antigen biosynthesis and their expression within the human population. We also consider the evolutionary selective pressures, e.g. malaria, that may account for the variation in carbohydrate structures and the implications of this biology for human disease.

Adaptations to water stress and pastoralism in the Turkana of northwest Kenya

The Turkana people inhabit arid regions of east Africa-where temperatures are high and water is scarce-and they practice subsistence pastoralism, such that their diet is primarily composed of animal products. Working with Turkana communities, we sequenced 367 genomes and identified 8 regions putatively involved in adaptation to water stress and pastoralism. One of these regions includes a putative enhancer for STC1-a kidney-expressed gene involved in the response to dehydration and the metabolism of purine-rich foods such as red meat. We show that STC1 is induced by antidiuretic hormone in humans, is associated with urea levels in the Turkana themselves, and is under strong selection in this population (s∼0.041). This work highlights that partnerships with subsistence-level groups can lead to new models of human physiology with biomedical relevance.

Natural selection of immune and metabolic genes associated with health in two lowland Bolivian populations

A growing body of work has addressed human adaptations to diverse environments using genomic data, but few studies have connected putatively selected alleles to phenotypes, much less among underrepresented populations such as Amerindians. Studies of natural selection and genotype-phenotype relationships in underrepresented populations hold potential to uncover previously undescribed loci underlying evolutionarily and biomedically relevant traits. Here, we worked with the Tsimane and the Moseten, two Amerindian populations inhabiting the Bolivian lowlands. We focused most intensively on the Tsimane, because long-term anthropological work with this group has shown that they have a high burden of both macro and microparasites, as well as minimal cardiometabolic disease or dementia. We therefore generated genome-wide genotype data for Tsimane individuals to study natural selection, and paired this with blood mRNA-seq as well as cardiometabolic and immune biomarker data generated from a larger sample that included both populations. In the Tsimane, we identified 21 regions that are candidates for selective sweeps, as well as 5 immune traits that show evidence for polygenic selection (e.g., C-reactive protein levels and the response to coronaviruses). Genes overlapping candidate regions were strongly enriched for known involvement in immune-related traits, such as abundance of lymphocytes and eosinophils. Importantly, we were also able to draw on extensive phenotype information for the Tsimane and Moseten and link five regions (containing PSD4, MUC21 and MUC22, TOX2, ANXA6, and ABCA1) with biomarkers of immune and metabolic function. Together, our work highlights the utility of pairing evolutionary analyses with anthropological and biomedical data to gain insight into the genetic basis of health-related traits.

Population designations in biomedical research: Limitations and perspectives

In biomedical research, population differences are of central interest. Variations in the frequency and severity of diseases and in treatment effects among human subpopulation groups are common in many medical conditions. Unfortunately, the practices in terms of subpopulation labeling do not exhibit the level of rigor one would expect in biomedical research, especially when studying multifactorial diseases such as cancer or atherosclerosis. The reporting of population differences in clinical research is characterized by large disparities in practices, and fraught with methodological issues and inconsistencies. The actual designations such as "Black" or "Asian" refer to broad and heterogeneous groups, with a great discrepancy among countries. Moreover, the use of obsolete concepts such as "Caucasian" is unfortunate and imprecise. The use of adequate labeling to reflect the scientific hypothesis needs to be promoted. Furthermore, the use of "race/ethnicity" as a unique cause of human heterogeneity may distract from investigating other factors related to a medical condition, particularly if this label is employed as a proxy for cultural habits, diet, or environmental exposure. In addition, the wide range of opinions among researchers does not facilitate the attempts made for resolving this heterogeneity in labeling. "Race," "ethnicity," "ancestry," "geographical origin," and other similar concepts are saturated with meanings. Even if the feasibility of a global consensus on labeling seems difficult, geneticists, sociologists, anthropologists, and ethicists should help develop policies and practices for the biomedical field.

Circulating thrifty microRNA is related to insulin sensitivity, adiposity, and energy metabolism in adults with overweight and obesity: the POUNDS Lost trial

BACKGROUND

MicroRNA 128-1 (miR-128-1) was recently linked to the evolutionary adaptation to famine and identified as a thrifty microRNA that controls energy expenditure, contributing to obesity and impaired glucose metabolism.

OBJECTIVES

We investigated whether circulating miR-128-1-5p and its temporal changes in response to weight-loss diet interventions were related to regulating insulin resistance, adiposity, and energy expenditure in adults with overweight and obesity. We also examined whether habitual physical activity (PA) and different macronutrient intakes modified associations of changes in miR-128-1-5p with improved metabolic outcomes.

METHODS

This study included 495 adults who consumed weight-loss diets with different macronutrient intakes. Circulating levels of miR-128-1-5p were assessed at baseline and 6 mo after the interventions. Outcome measurements included changes in insulin resistance HOMA-IR, adiposity, and resting energy expenditure.

RESULTS

We observed significant relations between circulating miR-128-1-5p and the positive selection signals at the 2q21.3 locus assessed by the single nucleotide polymorphisms rs1446585 and rs4988235. Higher miR-128-1-5p levels were associated with greater HOMA-IR (β per 1 SD: 0.08 [SE 0.03]; P = 0.009), waist circumference (β, 1.16 [0.55]; P = 0.036), whole-body total % fat mass (β, 0.75 [0.30]; P = 0.013), and REE (β, 23 [11]; P = 0.037). In addition, higher miR-128-1-5p level was related to lower total PA index (β, -0.23 [0.07]; P = 0.001) and interacted with PA (Pinteraction < 0.05) on changes in HOMA-IR and adiposity. We found that greater increases in miR-128-1-5p levels after the interventions were associated with lesser improvements in HOMA-IR and adiposity in participants with no change/decreases in PA. Furthermore, we found that dietary fat (Pinteraction = 0.027) and protein (Pinteraction= 0.055) intakes modified relations between changes in miR-128-1-5p and REE.

CONCLUSIONS

Circulating thrifty miRNA was linked to regulating body fat, insulin resistance, and energy metabolism. Temporal changes in circulating miR-128-1-5p were associated with better weight-loss outcomes during the interventions; habitual PA and dietary macronutrient intake may modify such relations. This trial was registered at clinicaltrials.gov as NCT00072995.

Modeling the spatiotemporal spread of beneficial alleles using ancient genomes

Ancient genome sequencing technologies now provide the opportunity to study natural selection in unprecedented detail. Rather than making inferences from indirect footprints left by selection in present-day genomes, we can directly observe whether a given allele was present or absent in a particular region of the world at almost any period of human history within the last 10,000 years. Methods for studying selection using ancient genomes often rely on partitioning individuals into discrete time periods or regions of the world. However, a complete understanding of natural selection requires more nuanced statistical methods which can explicitly model allele frequency changes in a continuum across space and time. Here we introduce a method for inferring the spread of a beneficial allele across a landscape using two-dimensional partial differential equations. Unlike previous approaches, our framework can handle time-stamped ancient samples, as well as genotype likelihoods and pseudohaploid sequences from low-coverage genomes. We apply the method to a panel of published ancient West Eurasian genomes to produce dynamic maps showcasing the inferred spread of candidate beneficial alleles over time and space. We also provide estimates for the strength of selection and diffusion rate for each of these alleles. Finally, we highlight possible avenues of improvement for accurately tracing the spread of beneficial alleles in more complex scenarios.

Parallel evolution in human populations: A biocultural perspective

Parallel evolution-where different populations evolve similar traits in response to similar environments-has been a topic of growing interest to biologists and biological anthropologists for decades. Parallel evolution occurs in human populations thanks to myriad biological and cultural mechanisms that permit humans to survive and thrive in diverse environments worldwide. Because humans shape and are shaped by their environments, biocultural approaches that emphasize the interconnections between biology and culture are key to understanding parallel evolution in human populations as well as the nuances of human biological variation and adaptation. In this review, we discuss how biocultural theory has been and can be applied to studies of parallel evolution and adaptation more broadly. We illustrate this through four examples of parallel evolution in humans: malaria resistance, lactase persistence, cold tolerance, and high-altitude adaptation.