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ABSTRACT Characterizing DNA methylation patterns is important for addressing key questions in evolutionary biology, geroscience, and medical genomics. While costs are decreasing, whole-genome DNA methylation profiling remains prohibitively expensive for most population-scale studies, creating a need for cost-effective, reduced representation approaches (i.e., assays that rely on microarrays, enzyme digests, or sequence capture to target a subset of the genome). Most common whole genome and reduced representation techniques rely on bisulfite conversion, which can damage DNA resulting in DNA loss and sequencing biases. Enzymatic methyl sequencing (EM-seq) was recently proposed to overcome these issues, but thorough benchmarking of EM-seq combined with cost-effective, reduced representation strategies has not yet been performed. To do so, we optimized Targeted Methylation Sequencing protocol (TMS)—which profiles ∼4 million CpG sites—for miniaturization, flexibility, and multispecies use at a cost of ∼$80. First, we tested modifications to increase throughput and reduce cost, including increasing multiplexing, decreasing DNA input, and using enzymatic rather than mechanical fragmentation to prepare DNA. Second, we compared our optimized TMS protocol to commonly used techniques, specifically the Infinium MethylationEPIC BeadChip (n=55 paired samples) and whole genome bisulfite sequencing (n=6 paired samples). In both cases, we found strong agreement between technologies (R² = 0.97 and 0.99, respectively). Third, we tested the optimized TMS protocol in three non-human primate species (rhesus macaques, geladas, and capuchins). We captured a high percentage (mean=77.1%) of targeted CpG sites and produced methylation level estimates that agreed with those generated from reduced representation bisulfite sequencing (R² = 0.98). Finally, we applied our protocol to profile age-associated DNA methylation variation in two subsistence-level populations—the Tsimane of lowland Bolivia and the Orang Asli of Peninsular Malaysia—and found age-methylation patterns that were strikingly similar to those reported in high income cohorts, despite known differences in age-health relationships between lifestyle contexts. Altogether, our optimized TMS protocol will enable cost-effective, population-scale studies of genome-wide DNA methylation levels across human and non-human primate species. 

Abstract Female social relationships are often shaped by the distribution of dietary resources. Socioecological models predict that females should form strict linear dominance hierarchies when resources are clumped and exhibit more egalitarian social structures when resources are evenly distributed. While many frugivores and omnivores indeed exhibit dominance hierarchies accompanied by differential resource access, many folivores deviate from the expected pattern and display dominance hierarchies despite evenly distributed resources. Among these outliers, geladas (Theropithecus gelada) present a conspicuous puzzle; females exhibit aggressive competition and strict dominance hierarchies despite feeding primarily on non-monopolizable grasses. However, these grasses become scarce in the dry season and geladas supplement their diet with underground storage organs that require relatively extensive energy to extract. We tested whether female dominance hierarchies provide differential access to underground storage organs by assessing how rank, season, and feeding context affect aggression in geladas under long-term study in the Simien Mountains National Park, Ethiopia. We found that the likelihood of receiving aggression was highest when feeding belowground and that the inverse relationship between rank and aggression was the most extreme while feeding belowground in the dry season. These results suggest that aggression in geladas revolves around belowground foods, which may mean that underground storage organs are an energetically central dietary component (despite being consumed less frequently than grasses), or that even “fallback” foods can influence feeding competition and social relationships. Further work should assess whether aggression in this context is directly associated with high-ranking usurpation of belowground foods from lower-ranking females following extraction. 

Abstract Neopterin, a product of activated white blood cells, is a marker of nonspecific inflammation that can capture variation in immune investment or disease-related immune activity and can be collected noninvasively in urine. Mounting studies in wildlife point to lifetime patterns in neopterin related to immune development, aging, and certain diseases, but rarely are studies able to assess whether neopterin can capture multiple concurrent dimensions of health and disease in a single system. We assessed the relationship between urinary neopterin stored on filter paper and multiple metrics of health and disease in wild geladas (Theropithecus gelada), primates endemic to the Ethiopian highlands. We tested whether neopterin captures age-related variation in inflammation arising from developing immunity in infancy and chronic inflammation in old age, inflammation related to intramuscular tapeworm infection, helminth-induced anti-inflammatory immunomodulation, and perturbations in the gastrointestinal microbiome. We found that neopterin had a U-shaped relationship with age, no association with larval tapeworm infection, a negative relationship with metrics related to gastrointestinal helminth infection, and a negative relationship with microbial diversity. Together with growing research on neopterin and specific diseases, our results demonstrate that urinary neopterin can be a powerful tool for assessing multiple dimensions of health and disease in wildlife. 

Across mammals, fertility and offspring survival are often lowest at the beginning and end of females’ reproductive careers. However, extrinsic drivers of reproductive success—including infanticide by males—could stochastically obscure these expected age-related trends. Here, we modelled reproductive ageing trajectories in two cercopithecine primates that experience high rates of male infanticide: the chacma baboon (Papio ursinus) and the gelada (Theropithecus gelada). We found that middle-aged mothers generally achieved the shortest interbirth intervals in chacma baboons. By contrast, old gelada females often showed shorter interbirth intervals than their younger group-mates with one exception: the oldest females typically failed to produce additional offspring before their deaths. Infant survival peaked in middle-aged mothers in chacma baboons but in young mothers in geladas. While infant mortality linked with maternal death increased as mothers aged in both species, infanticide risk did not predictably shift with maternal age. Thus, infanticide patterns cannot explain the surprising young mother advantage observed in geladas. Instead, we argue that this could be a product of their graminivorous diets, which might remove some energetic constraints on early reproduction. In sum, our data suggest that reproductive ageing is widespread but may be differentially shaped by ecological pressures.