Biology subjects

Lea, A. J.

Publications and source records attributed to Lea, A. J..

At least 19 recordsLinked to original sources

bioRxiv2026

Accelerated Evolution of Context-Dependent Gene Expression in Primate Immune Cells

Regulatory variation is widely recognized as a driver of evolution within and between species, including in the primate lineage. Evidence for potentially adaptive regulatory evolution in primates comes from both sequence-based tests for selection and cross-species comparisons of gene expression. However, comparative studies of gene expression have tended to focus on baseline cellular states, despite growing evidence that context-dependent gene regulation is important. Here, we investigate the evolution of gene expression in lymphoblastoid cell lines (LCLs) from 6 primate lineages (humans, chimpanzees, bonobos, western gorillas, Sumatran orangutans, and rhesus macaques) using data from both control and 5 perturbed cellular conditions (n=22-25 individuals per condition). Analyzing baseline expression data, we find that genes involved in immunity often exhibit lineage-specific transcriptional shifts, and that these genes occur near regions with lineage-specific sequence acceleration and lineage-specific epigenomic states. However, the subset of genes that respond to in vitro perturbations have evolved at significantly higher rates than environmentally-insensitive genes, a finding we replicate in an independent four-species dataset of primary white blood cells (n=26). Together, our findings support the argument that focusing on baseline states alone provides a biased view of gene regulatory evolution, and suggest that studying gene regulation in dynamic contexts can enrich our understanding of primate evolution.

evolutionary biology↗

bioRxiv2026

Evaluating performance bias in face-to-BMI vision transformer models across diverse human populations

Computer vision models that estimate body mass index (BMI) from facial features offer a non-invasive, low-cost alternative to physical measurement, with uses in telemedicine, emergency care where a scale or measuring tools arent available, automated self-monitoring, and large-scale epidemiological research. Most of these models, however, are trained on government records, social media images, and celebrity photographs, sources that introduce dataset biases and fail to represent the general public. This study tests how well a face-to-BMI machine learning model generalizes across populations, specifically how morphological diversity and population-specific training data affect cross-cultural accuracy. We trained and evaluated Vision Transformer (ViT-H/14) models on paired BMI measurements and facial photographs from four Indigenous populations: the Orang Asli of Malaysia, the Ju/hoansi of Southern Africa, the Sama residing in the Philippines, and the Tsimane of Bolivia. To evaluate how training data composition affects predictions, we compared four training strategies, from single-population models (focal models) to models trained on the full combined global dataset (global models). In-distribution training always produced the best performance. Models exposed to a target populations morphology, whether focal or global, consistently predicted BMI most accurately for that population. But when a target population differed from the training sample, adding more cross-cultural variation to training improved out-of-distribution predictions. Therefore, training on a populations own data works best when that data exists, and training on data spanning a wide range of human morphology is the strongest fallback when it doesnt. These findings suggest that while target population training data produces the most accurate results, training on datasets that capture global morphological variation substantially improves performance in unrepresented populations. Broader diversity in training data is essential for developing machine learning health tools that generalize reliably across human populations.

bioinformatics↗

bioRxiv2026

Early and current environments exert distinct effects on immune function in the Orang Asli

Humans evolved in environments characterized by subsistence foraging and hunting, high levels of physical activity, and regular and diverse pathogen exposure. Industrialization has rapidly altered these environments, leading to increased metabolic and inflammatory disease risk. These observations have motivated studies of how industrialization shapes immune function, but whether industrialization alters immune biology through developmental embedding of early-life environments or ongoing plastic responses to current conditions remains poorly understood. To address this gap, we worked with the Orang Asli--the Indigenous peoples of Peninsular Malaysia--who currently span a gradient from subsistence horticulture, foraging, and hunting to industrialized, urban environments with substantial inter-individual variation in life course experiences. Leveraging continuous measures of both early-life and current lifestyle, we found that current lifestyle exerts stronger effects on adult immune gene expression than early-life conditions, impacting 1,428 as compared to 223 genes, respectively. Early-life associated genes were enriched for pathways regulating adaptive immunity, particularly T cell development and differentiation, consistent with higher predicted T cell abundance and circulating IL-8 in urban-born individuals. In contrast, current exposure to urban, industrialized conditions was linked to innate immune and inflammatory activation, including dendritic cell abundance, metabolic pathway upregulation, and elevated CRP. Finally, consistent with lower rates of immune disorders in non-industrial settings, current exposure to this lifestyle was associated with up-regulation of genes involved in Th1/Th2 differentiation. Together, these results emphasize that industrialized immune profiles reflect both early-life developmental embedding and ongoing environmental responses, highlighting the importance of considering exposures across the life course. Significance statementHumans evolved in environments with high levels of physical activity, subsistence-based diets, and constant pathogen exposure. Rapid industrialization has dramatically changed these conditions, coinciding with rising rates of non-communicable diseases with inflammatory underpinnings. Our study with the Orang Asli, the Indigenous peoples of Peninsular Malaysia, tests how exposure to industrialization across the life course shapes immune variation. We find that early-life environments leave lasting marks on adaptive immune function particularly T cells, while industrialized adult lifestyle influences innate immune activity and inflammation. These results clarify how different stages of life contribute to immune remodeling and point to a mechanistic link between industrialization and disease risk, highlighting the importance of both early-life and current environments in shaping later life health.

genetics↗

bioRxiv2026

Rhodopsin is a tunable capacitor buffering the toxic, desensitizing retinoids of the vertebrate eye

The eye is a marvel of evolution, but visual sensitivity introduces the risk of blinding photodamage. Here we reveal that the locus of sensitivity--the visual pigment rhodopsin --moonlights as a tunable mechanism of retinal photoprotection. Independent of signaling, light activated rhodopsin (R*) serves as an overflow capacitor buffering all-trans retinal (atRAL), a toxic and desensitizing retinoid agonist that accumulates as lipofuscin--a clinical marker of macular degeneration. Across mammals, R* stability reflects binding affinity and sequestration of atRAL (capacitance), thereby mitigating phototoxicity to a degree proportional to species photodamage risk, with human R* uniquely non-protective. A mouse model of defective atRAL clearance treated with a synthetic R* of unnaturally high atRAL capacitance preserved retinal function following light damage. This gene therapy also provided supra-physiological scotopic sensitivity despite being a signal-silent receptor, shielding neighboring dark-state receptors from agonist interference during regeneration, while also enhancing the signaling of endogenous R*. While the consensus human rhodopsin is not photoprotective, during recent evolution, mutations that protect against light damage emerged in high irradiance human environments and are now significantly associated with a 38% reduced risk of blindness and low vision. Together, our findings redefine rhodopsin as a tunable light buffer that can be leveraged to enhance photoreceptor function beyond natural limits.

biochemistry↗

bioRxiv2026

Development and assessment of tailored illustrations to enhance community understandings of genetics topics

ObjectivesEffective communication about genetics concepts is essential for collaborative anthropological genetics research. However, communication can be challenging because many ideas are abstract and may be especially unfamiliar to communities with limited access to formal education. Indeed, there are no widely adopted models for communicating such information, nor a clear understanding of the social factors that may shape participant engagement. Here, we conducted a qualitative and quantitative, community-driven study to understand how illustrations can be useful to support concept sharing with two Indigenous groups--the Orang Asli of Peninsular Malaysia and the Turkana of Kenya. MethodsWe used a two phase approach to create and evaluate how illustrations can bolster communication about genetics concepts. First, we created images illustrating answers to frequently asked questions about genetics, iteratively updating the illustrations based on participant feedback. Second, we conducted 92 interviews to evaluate the finalized illustrations effectiveness. Finally, we analyzed the interview data using thematic analyses, multivariable modeling, and multiple correspondence analyses to identify patterns in participant understanding and feedback, including age, sex, market integration, and schooling. ResultsParticipants reported high interest in genetics research (92%) and broadly positive perceptions of the illustrations. Familiar, locally-grounded imagery was preferred and associated with greater perceived clarity, while more technical illustrations were more frequently reported as confusing. Quantitative analyses showed strong internal consistency across measures of engagement and understanding, with modest variation by degree of market-integration, schooling, and sex. DiscussionOur findings demonstrate that community-specific visualizations, co-developed through iterative feedback, can effectively support engagement with genetics research in participant communities.

scientific communication and education↗

bioRxiv2026

Divergent Biological Consequences of APOE Isoforms Across Industrialized and Non-Industrial Environments

The apolipoprotein {varepsilon}4 (APOE {varepsilon}4) isoform directly alters cholesterol and immune biology and is associated with an increased risk of neurodegenerative and cardiometabolic disease in industrialized settings; nevertheless, APOE {varepsilon}4--which is ancestral in humans--has persisted over evolutionary time. One potential explanation is that the costs and benefits of APOE {varepsilon}4 were significantly different in the environments in which humans evolved compared to those we experience today. In support, previous work has suggested that living in a high pathogen environment, engaging in high levels of physical activity, or eating a low fat diet can dampen the detrimental effects of APOE {varepsilon}4, and has revealed positive effects for fertility. However, direct tests of whether APOE isoforms are associated with different biological outcomes in non-industrial versus industrialized contexts are lacking. Working with the Turkana of Kenya and the Orang Asli of Peninsular Malaysia--two Indigenous groups in which individuals of shared ancestry span a continuum of subsistence, non-industrial to urban, industrialized lifestyles--we investigated how APOE genotypes impact cholesterol, immunological, and reproductive traits and tested for genotype x environment (GxE) interactions. First, we confirmed established genotype effects across lifestyles, showing that more APOE {varepsilon}4 alleles are associated with higher total cholesterol, higher LDL cholesterol, and lower HDL cholesterol. Second, we tested for lifestyle interactions, finding lifestyle-dependent effects of genotype on innate immune biomarkers in the Orang Asli but not Turkana. Finally, we show that more APOE {varepsilon}4 alleles are correlated with an extended reproductive lifespan, however this effect is relatively weak, is not consistent across populations, and does not correspond with a higher reproductive output. Together, our study provides evidence that industrialized environments can modify the biology of APOE {varepsilon}4; however, we find that APOE {varepsilon}4 is not universally beneficial in non-industrial contexts, highlighting the role of local environmental variation in determining its specific costs and benefits.

evolutionary biology↗

bioRxiv2025

Early life adversity shapes life history trade-offs between growth and reproduction in free-ranging rhesus macaques

Life history theory predicts that organisms allocate resources across physiological processes to maximize fitness. Under this framework, early life adversity (ELA)--which often limits energetic capital--could shape investment in growth and reproduction, as well as trade-offs between them, ultimately contributing to variation in evolutionary fitness. Using long-term demographic, behavioral, and physiological data for 2,100 females from a non-human primate population, we tested whether naturally-occurring ELA influences investment in the competing physiological demands of growth and reproduction. By analyzing ELA, growth, and reproduction in the same individuals, we also assessed whether adversity intensifies trade-offs between life history domains. We found that ELA influenced life history patterns, and was associated with modified growth, delayed reproductive maturity, and small adult body size. Different types of ELA sometimes had distinct reproductive outcomes--e.g., large group size was linked to faster reproductive rates, while low maternal rank predicted slower ones. Adversity also amplified trade-offs between growth and reproduction: small body size was a stronger predictor of delayed and reduced reproductive output in females exposed to ELA, compared to those not exposed. Finally, we examined how traits modified by ELA related to lifetime reproductive success. Across the population, starting reproduction earlier and maintaining a moderate reproductive rate conferred the greatest number of offspring surviving to reproductive maturity. These findings suggest that ELA impacts key life history traits as well as relationships between them, and can constrain individuals from adopting the most optimal reproductive strategy. Significance StatementEarly life adversity (ELA) can have lasting effects on evolutionary fitness (e.g., the number of surviving offspring an animal produces); however, the paths connecting ELA to fitness--for example by influencing growth, reproductive timing or rate, or trade-offs between these processes--remain unclear. Leveraging long-term behavioral, physiological, and demographic data from 2,100 female rhesus macaques, we found that ELA-exposed females exhibited growth and reproductive schedules associated with less-optimal lifetime fitness outcomes. Further, ELA intensified trade-offs between growth and reproduction, suggesting that affected individuals face steeper energetic constraints. Our findings highlight the long-lasting impacts of ELA on traits of evolutionary and biomedical importance in a non-human primate model with relevance to humans.

evolutionary biology↗

bioRxiv2025

Recent lifestyle change impacts sleep and circadian rhythms among the Indigenous peoples of Peninsular Malaysia

Sleep disorders are rising globally, but their lifestyle causes remain unclear. We recorded sleep-wake patterns via actigraphy from 1036 Orang Asli adults across 12 communities in Peninsular Malaysia undergoing market integration, marked by changes in permanent infrastructure (electricity and housing), digital technologies (smartphones), and labor practices (i.e., wage labor). We evaluated associations with sleep timing (onset, offset and regularity), quality (nighttime awakenings and waking after sleep onset) and quantity (sleep duration), while accounting for age and sex. Delayed and destabilized sleep timing was observed in communities with powerline access, also resulting in shorter sleep duration; paradoxically, it also improved sleep quality, suggesting increased homeostatic pressure. Age and sex were strong and consistent predictors of sleep variation: older adults had earlier, shorter, and more consistent, consolidated sleep patterns. Men displayed later and shorter sleep patterns than women, likely reflecting gendered divisions of labor among the Orang Asli. Despite averaging relatively few hours slept (6 hrs), Orang Asli exhibited relatively efficient sleep, potentially challenging the notion that longer sleep is universally beneficial. These findings underscore the complex interplay of biology, ecology, and culture in shaping sleep and circadian rhythms. SignificanceA comprehensive cross-sectional study of sleep across a pronounced lifestyle gradient among Malaysias Indigenous Orang Asli populations reveals new insights into the drivers of human sleep and circadian rhythms. Lifestyle changes with market integration, particularly access to electricity, resulted in delayed bedtime and shortened sleep duration, yet enhanced sleep consolidation. Consistent with cross-cultural evidence, aging resulted in earlier bedtimes, earlier rising times, and less sleep. Our findings contribute to debates about the adaptability of human circadian rhythms and challenge universal models of optimal sleep duration.

physiology↗

bioRxiv2025

Age and early life adversity shape heterogeneity of the epigenome across tissues in macaques

Age and early life adversity (ELA) are both key determinants of health, but whether they target similar physiological mechanisms across the body is unknown due to limited multi-tissue datasets from well-characterized cohorts. We generated DNA methylation (DNAm) profiles across 14 tissues in 237 semi-free ranging rhesus macaques, with records of naturally occurring ELA. We show that age-associated DNAm variation is predominantly tissue-dependent, yet tissue-specific epigenetic clocks reveal that the pace of epigenetic aging is relatively consistent within individuals. ELA effects on loci are adversity-dependent, but a given ELA has a coordinated impact across tissues. Finally, ELA targeted many of the same loci as age, but the direction of these effects varied, indicating that ELA does not uniformly contribute to accelerated age in the epigenome. ELA thus imprints a coordinated, tissue-spanning epigenetic signature that is both distinct from and intertwined with age-related change, advancing our understanding of how early environments sculpt the molecular foundations of aging and disease.

genomics↗

bioRxiv2025

Early life environments shape adult cardiometabolic health during rapid lifestyle change

Early life environments can have long-lasting impacts on health and fitness, but the evolutionary significance of these effects remains debated. Two major classes of explanations have been proposed: developmental constraints (DC) explanations posit that early life adversity limits optimal development, leading to long-term costs, while predictive adaptive response (PAR) explanations posit that organisms use early life cues to predict adult conditions, resulting in detriments when adult environments do not match expectations. We tested these hypotheses using anthropological and biomedical data for the Orang Asli--the Indigenous peoples of Peninsular Malaysia--who are undergoing a rapid but heterogenous transition from non-industrial, subsistence-based livelihoods to more industrialized, market-integrated conditions. Using questionnaire data, we show that this shift creates natural variation in the degree of similarity between early life and adult environments. Using anthropometric and health data, we find that, more rural, subsistence-based early life environments are associated with shorter stature but better adult cardiometabolic health. Applying a quadratic regression framework, we find support for DC but not PAR in explaining adult cardiometabolic health, echoing findings and conclusions from other long-lived species. Overall, our results suggest that early life conditions can provide additive protection against common health issues associated with urban, industrialized lifestyle exposure.

evolutionary biology↗

bioRxiv2024

Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes

A major goal in evolutionary biology and biomedicine is to understand the complex interactions between genetic variants, the epigenome, and gene expression. However, the causal relationships between these factors remain poorly understood. mSTARR-seq, a methylation-sensitive massively parallel reporter assay, is capable of identifying methylation-dependent regulatory activity at many thousands of genomic regions simultaneously, and allows for the testing of causal relationships between DNA methylation and gene expression on a region-by-region basis. Here, we developed a multiplexed mSTARR-seq protocol to assay naturally occurring human genetic variation from 25 individuals sampled from 10 localities in Europe and Africa. We identified 6,957 regulatory elements in either the unmethylated or methylated state, and this set was enriched for enhancer and promoter annotations, as expected. The expression of 58% of these regulatory elements was modulated by methylation, which was generally associated with decreased RNA expression. Within our set of regulatory elements, we used allele-specific expression analyses to identify 8,020 sites with genetic effects on gene regulation; further, we found that 42.3% of these genetic effects varied between methylated and unmethylated states. Sites exhibiting methylation-dependent genetic effects were enriched for GWAS and EWAS annotations, implicating them in human disease. Compared to datasets that assay DNA from a single European individual, our multiplexed assay uncovers dramatically more genetic effects and methylation-dependent genetic effects, highlighting the importance of including diverse individuals in assays which aim to understand gene regulatory processes.

genomics↗

bioRxiv2024

Testing frameworks for early life effects: the developmental constraints and adaptive responsehypotheses do not explain key fertility outcomes in wild female baboons

In evolutionary ecology, two classes of explanations are frequently invoked to explain "early life effects" on adult outcomes. Developmental constraints (DC) explanations contend that costs of early adversity arise from limitations adversity places on optimal development. Adaptive response (AR) hypotheses propose that later life outcomes will be worse when early and adult environments are poorly "matched." Here, we use recently proposed mathematical definitions for these hypotheses and a quadratic-regression based approach to test the long-term consequences of variation in developmental environments on fertility in wild baboons. We evaluate whether low rainfall and/or dominance rank during development predict three female fertility measures in adulthood, and whether any observed relationships are consistent with DC and/or AR. Neither rainfall during development nor the difference between rainfall in development and adulthood predicted any fertility measures. Females who were low-ranking during development had an elevated risk of losing infants later in life, and greater change in rank between development and adulthood predicted greater risk of infant loss. However, both effects were statistically marginal and consistent with alternative explanations, including adult environmental quality effects. Consequently, our data do not provide compelling support for either of these common explanations for the evolution of early life effects.

evolutionary biology↗

bioRxiv2024

Sex differences in immune function and disease risk are not easily explained by an evolutionary mismatch

The "Pregnancy Compensation Hypothesis" (PCH) posits that sex differences in the mammalian immune system reflect the effects of selection on female immunity during pregnancy, during which increased immunomodulation is required to reduce immune responses to the fetus, while maintaining the ability to respond to pathogens. In humans, fewer pathogens and lower parity in urban, industrialized environments has been suggested to leave female immune systems under-stimulated, creating an "evolutionary mismatch" which exacerbates sex differences in immunity and increases female autoimmune disease risk. Yet, robust tests of this mismatch hypothesis have not been conducted. Here, we first confirmed a sex-bias in autoimmune disease prevalence in a large dataset of individuals from the United Kingdom (UK Biobank). Second, we asked whether sex differences in immune function are affected by shifts toward urban, lower-parity lifestyles in a single population--the Turkana people of northwest Kenya. We found that lifestyle alters sex differences in immune cell type proportions, but not in gene expression levels. Contrary to expectations from the PCH, parity did not predict immune physiology. We then tested for generalizable trends across natural fertility mammalian populations versus urban humans (data from Turkana, NHANES, GTEx, Batwa and Bakiga, yellow baboons, and macaques). We did not find consistent relationships between lifestyle and sex-biases in immune biomarkers or between parity and the same immune outcomes. Indeed, we found that parity predicts autoimmune disease risk in the opposite direction than expected from the PCH, with higher parity associated with higher autoimmune disease risk while adjusting for relevant socioeconomic variables in the UK Biobank. Taken together, our work suggests that while sex clearly influences immune physiology and disease risk in urban settings, these effects are not easily explained by an evolutionary mismatch. Future work addressing how sex interacts with lifestyle change to generate disease is needed.

evolutionary biology↗

bioRxiv2023

Early life adversity has sex-dependent effects on survival across the lifespan in rhesus macaques

Exposure to adversity during early life is linked to lasting detrimental effects on evolutionary fitness across many taxa. However, due to the challenges of collecting longitudinal data, especially in species where one sex disperses, direct evidence from long-lived species remains relatively scarce. Here we test the effects of early life adversity on male and female longevity in a free-ranging population of rhesus macaques (Macaca mulatta) at Cayo Santiago, Puerto Rico. We leveraged six decades of data to quantify the relative importance of ten forms of early life adversity for 6,599 macaques (3,230 male, 3,369 female), with a smaller sample size (N=299) for one form of adversity (maternal social isolation) which required high-resolution behavioral data. We found that individuals who experienced more early life adversity died earlier than those who experienced less adversity. Mortality risk was highest during early life, defined as birth to four years old, suggesting acute survival effects of adversity, but heightened mortality risk was also present in macaques who survived to adulthood. Females and males were affected differently by some forms of adversity, and these differences might be driven by varying energetic demands, female philopatry, and male dispersal. By leveraging data on thousands of macaques collected over decades, our results show that the fitness consequences of early life adversity are not uniform across individuals but vary as a function of the type of adversity, timing, and social context, and thus contribute to our limited but growing understanding of the evolution of early life sensitivities in long-lived species. Significance Statement Exposure to early life adversity, even when conditions subsequently improve, can have profound and persistent consequences for human health. Negative effects of early life adversity appear widespread across the animal kingdom. To date, however, direct evidence from long-lived species is relatively scarce due to the difficulties of collecting data from early life till death. We leverage six decades of observations on thousands of free-ranging male and female rhesus macaques to examine the complex ways early life adversity impacts survival. Our results suggest that the type of adversity and life history factors intersect to impact immediate and downstream survival. By studying early life adversity across environments, cultures, contexts, and species, we can better understand the evolutionary underpinnings of early life sensitivities.

animal behavior and cognition↗

bioRxiv2023

DNA methylation signatures of early life adversity are exposure-dependent in wild baboons

The early life environment can profoundly shape the trajectory of an animals life, even years or decades later. One mechanism proposed to contribute to these early life effects is DNA methylation. However, the frequency and functional importance of DNA methylation in shaping early life effects on adult outcomes is poorly understood, especially in natural populations. Here, we integrate prospectively collected data on fitness-associated variation in the early environment with DNA methylation estimates at 477,270 CpG sites in 256 wild baboons. We find highly heterogeneous relationships between the early life environment and DNA methylation in adulthood: aspects of the environment linked to resource limitation (e.g., low-quality habitat, early life drought) are associated with many more CpG sites than other types of environmental stressors (e.g., low maternal social status). Sites associated with early resource limitation are enriched in gene bodies and putative enhancers, suggesting they are functionally relevant. Indeed, by deploying a baboon-specific, massively parallel reporter assay, we show that a subset of windows containing these sites are capable of regulatory activity, and that, for 88% of early drought-associated sites in these regulatory windows, enhancer activity is DNA methylation-dependent. Together, our results support the idea that DNA methylation patterns contain a persistent signature of the early life environment. However, they also indicate that not all environmental exposures leave an equivalent mark and suggest that socioenvironmental variation at the time of sampling is more likely to be functionally important. Thus, multiple mechanisms must converge to explain early life effects on fitness-related traits. Significance statementThe environment animals face when young can affect how they function throughout life. Long-lasting changes in DNA methylation--a chemical mark deposited on DNA that can affect gene activity--have been hypothesized to contribute to early life effects. But evidence for persistent, early environment-associated differences in DNA methylation is lacking in wild animals. Here, we show that early life adversity in wild baboons predicts DNA methylation levels in adulthood, especially for animals born in low resource environments and drought conditions. We also show that some of the changes we observe in DNA methylation have the capacity to influence gene activity levels. Together, our results support the idea that early experiences can become biologically embedded in the genomes of wild animals.

genomics↗

bioRxiv2023

DNA methylation-environment interactions in the human genome

Previously we showed that a massively parallel reporter assay, mSTARR-seq, could be used to simultaneously test for both enhancer-like activity and DNA methylation-dependent enhancer activity for millions of loci in a single experiment (Lea et al., 2018). Here we apply mSTARR-seq to query nearly the entire human genome, including almost all CpG sites profiled either on the commonly used Illumina Infinium MethylationEPIC array or via reduced representation bisulfite sequencing. We show that fragments containing these sites are enriched for regulatory capacity, and that methylation-dependent regulatory activity is in turn sensitive to the cellular environment. In particular, regulatory responses to interferon alpha (IFNA) stimulation are strongly attenuated by methyl marks, indicating widespread DNA methylation-environment interactions. In agreement, methylation-dependent responses to IFNA identified via mSTARR-seq predict methylation-dependent transcriptional responses to challenge with influenza virus in human macrophages. Our observations support the idea that pre-existing DNA methylation patterns can influence the response to subsequent environmental exposures--one of the tenets of biological embedding. However, we also find that, on average, sites previously associated with early life adversity are not more likely to functionally influence gene regulation than expected by chance.

genomics↗

bioRxiv2023

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.

evolutionary biology↗

bioRxiv2022

Chromatin activity identifies differential gene regulation across human ancestries

Current evidence suggests that cis-regulatory elements controlling gene expression may be the predominant target of natural selection in humans and other species. Detecting selection acting on these elements is critical to understanding evolution but remains challenging because we do not know which mutations will affect gene regulation. To address this, we devised an approach to search for lineage-specific selection on chromatin activity, transcription factor binding, and chromosomal looping--critical steps in transcriptional regulation. Applying this approach to lymphoblastoid cells from 831 individuals of either European or African descent, we find strong signals of differential chromatin activity linked to gene expression differences between ancestries in numerous contexts, but no evidence of functional differences in chromosomal looping. Moreover, we show that enhancers rather than promoters display the strongest signs of selection associated with sites of differential transcription factor binding. Overall, our study indicates that some cis-regulatory adaptation may be more easily detected at the level of chromatin than DNA sequence. This work provides a vast resource of genomic interaction data from diverse human populations and establishes a novel selection test that will benefit future study of regulatory evolution in humans and other species.

genomics↗