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1. Tracing demographic histories through time using ancient DNA in Chilean Fuego-Patagonia

   Balentine, C. M. ; Alfonso-Durruty, M. ; Reynolds, A. W. ; Vilar, M. ; Morello, F. ; San Román, M. ; Springs, L. C. ; Bolnick, D. A. ( January 2022 , American Journal of Biological Anthropology)

   Historically, hunter-gatherers living east and west of the Andean foothills of southern South America (Fuego-Patagonia) practiced different subsistence strategies. To the east, the wide open and relatively dry pampas presented a climate ideal for Terrestrial hunter-gatherers who depended on terrestrial animals (e.g., Lama guanicoe). In contrast, Marine hunter-gatherers who lived on islands in the western archipelago, a colder and wetter environment, mainly subsisted on marine resources (e.g., seals and shellfish). Archaeological evidence dates Terrestrial hunter-gatherers’ presence in Fuego-Patagonia to at least ~10,500 BP, whereas Marine hunter-gatherers’ presence dates to ~6,500 BP and is associated with highly specialized tools that have only been observed in the archaeological record after this time. Genetic analyses of some ancient Fuegian-Patagonians have supported the hypothesis that Marine hunter-gatherers migrated into the region after Terrestrial hunter-gatherers, around 6,500 BP (7,500 calBP), while analyses of other individuals suggest that Marine hunter-gatherers descended from the earlier Terrestrial hunter-gatherer groups. Here, we test these hypotheses by analyzing newly collected genome-wide data from n=46 ancient Chilean Fuegian-Patagonian individuals belonging to Marine, Terrestrial, and Mixed-economy archaeological sites dating to 6,895–304 calBP. We explored basic population structure among these hunter-gatherer groups using PCA and ADMIXTURE. We calculated π, pairwise-FST, and f-statistics, and developed demographic simulations to further examine genetic relationships among the groups. The results of this study shed light on local demographic patterns of ancient southern South American groups, which in turn provides more insight into broader population histories of South America. This study was funded by FONDECYT (Chile), National Geographic Society, National Science Foundation, and Wenner-Gren Foundation. C. M. Balentine is supported by an NSF Graduate Research Fellowship. 

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2. Complex variation of trabecular bone structure in the proximal humerus and femur of five modern human populations

   https://doi.org/10.1002/ajpa.23725  

   Doershuk, Lily J. ; Saers, Jaap P. P. ; Shaw, Colin N. ; Jashashvili, Tea ; Carlson, Kristian J. ; Stock, Jay T. ; Ryan, Timothy M. ( December 2018 , American Journal of Physical Anthropology)

   This project investigates trabecular bone structural variation in the proximal humerus and femur of hunter‐gatherer, mixed‐strategy agricultural, medieval, and human groups to address three questions: (a) What is the extent of trabecular bone structural variation in the humerus and femur between populations with different inferred activity levels? (b) How does variation in the proximal humerus relate to variation in the proximal femur? (c) Are trabecular bone microstructural variables sexually dimorphic?

   The proximal humerus and femur of 73 adults from five human groups with distinct subsistence strategies were scanned using a micro‐computed tomography system. Centralized volumes of interest within the humeral and femoral heads were extracted and analyzed to quantify bone volume fraction, trabecular thickness, trabecular separation, connectivity density, degree of anisotropy, and bone surface density.

   In the humerus and femur, groups with the highest inferred activity levels have higher bone volume fraction and trabecular thickness, and lower bone surface density than those with lower inferred activity levels. However, the humeral pattern does not exactly mirror that of the femur, which demonstrates a steeper gradient of difference between subsistence groups. No significant differences were identified in trabecular separation. No consistent patterns of sexual dimorphism were present in the humerus or femur.

   Reduced skeletal robusticity of proximal humeral and femoral trabecular bone corresponds with reduced activity level inferred from subsistence strategy. However, human trabecular bone structural variation is complex and future work should explore how other factors (diet, climate, genetics, disease load, etc.), in addition to activity, influence bone structural variation.

    

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3. Polyphenol Utilization Proteins in the Human Gut Microbiome

   https://doi.org/10.1128/AEM.01851-21  

   Zheng, Bo ; He, Yinchao ; Zhang, Pengxiang ; Huo, Yi-Xin ; Yin, Yanbin ( February 2022 , Applied and Environmental Microbiology)

   Ercolini, Danilo (Ed.)

   ABSTRACT Dietary polyphenols can significantly benefit human health, but their bioavailability is metabolically controlled by human gut microbiota. To facilitate the study of polyphenol metabolism for human gut health, we have manually curated experimentally characterized polyphenol utilization proteins (PUPs) from published literature. This resulted in 60 experimentally characterized PUPs (named seeds) with various metadata, such as species and substrate. Further database search found 107,851 homologs of the seeds from UniProt and UHGP (unified human gastrointestinal protein) databases. All PUP seeds and homologs were classified into protein classes, families, and subfamilies based on Enzyme Commission (EC) numbers, Pfam (protein family) domains, and sequence similarity networks. By locating PUP homologs in the genomes of UHGP, we have identified 1,074 physically linked PUP gene clusters (PGCs), which are potentially involved in polyphenol metabolism in the human gut. The gut microbiome of Africans was consistently ranked the top in terms of the abundance and prevalence of PUP homologs and PGCs among all geographical continents. This reflects the fact that dietary polyphenols are consumed by the African population more commonly than by other populations, such as Europeans and North Americans. A case study of the Hadza hunter-gatherer microbiome verified the feasibility of using dbPUP to profile metagenomic data for biologically meaningful discovery, suggesting an association between diet and PUP abundance. A Pfam domain enrichment analysis of PGCs identified a number of putatively novel PUP families. Lastly, a user-friendly web interface ( https://bcb.unl.edu/dbpup/ ) provides all the data online to facilitate the research of polyphenol metabolism for improved human health. IMPORTANCE Long-term consumption of polyphenol-rich foods has been shown to lower the risk of various human diseases, such as cardiovascular diseases, cancers, and metabolic diseases. Raw polyphenols are often enzymatically processed by gut microbiome, which contains various polyphenol utilization proteins (PUPs) to produce metabolites with much higher bioaccessibility to gastrointestinal cells. This study delivered dbPUP as an online database for experimentally characterized PUPs and their homologs in human gut microbiome. This work also performed a systematic classification of PUPs into enzyme classes, families, and subfamilies. The signature Pfam domains were identified for PUP families, enabling conserved domain-based PUP annotation. This standardized sequence similarity-based PUP classification system offered a guideline for the future inclusion of new experimentally characterized PUPs and the creation of new PUP families. An in-depth data analysis was further conducted on PUP homologs and physically linked PUP gene clusters (PGCs) in gut microbiomes of different human populations. 

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4. Evidence, causes, and consequences of declining nitrogen availability in terrestrial ecosystems

   https://doi.org/10.1126/science.abh3767  

   Mason, Rachel E. ; Craine, Joseph M. ; Lany, Nina K. ; Jonard, Mathieu ; Ollinger, Scott V. ; Groffman, Peter M. ; Fulweiler, Robinson W. ; Angerer, Jay ; Read, Quentin D. ; Reich, Peter B. ; et al ( April 2022 , Science)

   BACKGROUND The availability of nitrogen (N) to plants and microbes has a major influence on the structure and function of ecosystems. Because N is an essential component of plant proteins, low N availability constrains the growth of plants and herbivores. To increase N availability, humans apply large amounts of fertilizer to agricultural systems. Losses from these systems, combined with atmospheric deposition of fossil fuel combustion products, introduce copious quantities of reactive N into ecosystems. The negative consequences of these anthropogenic N inputs—such as ecosystem eutrophication and reductions in terrestrial and aquatic biodiversity—are well documented. Yet although N availability is increasing in many locations, reactive N inputs are not evenly distributed globally. Furthermore, experiments and theory also suggest that global change factors such as elevated atmospheric CO 2 , rising temperatures, and altered precipitation and disturbance regimes can reduce the availability of N to plants and microbes in many terrestrial ecosystems. This can occur through increases in biotic demand for N or reductions in its supply to organisms. Reductions in N availability can be observed via several metrics, including lowered nitrogen concentrations ([N]) and isotope ratios (δ 15 N) in plant tissue, reduced rates of N mineralization, and reduced terrestrial N export to aquatic systems. However, a comprehensive synthesis of N availability metrics, outside of experimental settings and capable of revealing large-scale trends, has not yet been carried out. ADVANCES A growing body of observations confirms that N availability is declining in many nonagricultural ecosystems worldwide. Studies have demonstrated declining wood δ 15 N in forests across the continental US, declining foliar [N] in European forests, declining foliar [N] and δ 15 N in North American grasslands, and declining [N] in pollen from the US and southern Canada. This evidence is consistent with observed global-scale declines in foliar δ 15 N and [N] since 1980. Long-term monitoring of soil-based N availability indicators in unmanipulated systems is rare. However, forest studies in the northeast US have demonstrated decades-long decreases in soil N cycling and N exports to air and water, even in the face of elevated atmospheric N deposition. Collectively, these studies suggest a sustained decline in N availability across a range of terrestrial ecosystems, dating at least as far back as the early 20th century. Elevated atmospheric CO 2 levels are likely a main driver of declines in N availability. Terrestrial plants are now uniformly exposed to ~50% more of this essential resource than they were just 150 years ago, and experimentally exposing plants to elevated CO 2 often reduces foliar [N] as well as plant-available soil N. In addition, globally-rising temperatures may raise soil N supply in some systems but may also increase N losses and lead to lower foliar [N]. Changes in other ecosystem drivers—such as local climate patterns, N deposition rates, and disturbance regimes—individually affect smaller areas but may have important cumulative effects on global N availability. OUTLOOK Given the importance of N to ecosystem functioning, a decline in available N is likely to have far-reaching consequences. Reduced N availability likely constrains the response of plants to elevated CO 2 and the ability of ecosystems to sequester carbon. Because herbivore growth and reproduction scale with protein intake, declining foliar [N] may be contributing to widely reported declines in insect populations and may be negatively affecting the growth of grazing livestock and herbivorous wild mammals. Spatial and temporal patterns in N availability are not yet fully understood, particularly outside of Europe and North America. Developments in remote sensing, accompanied by additional historical reconstructions of N availability from tree rings, herbarium specimens, and sediments, will show how N availability trajectories vary among ecosystems. Such assessment and monitoring efforts need to be complemented by further experimental and theoretical investigations into the causes of declining N availability, its implications for global carbon sequestration, and how its effects propagate through food webs. Responses will need to involve reducing N demand via lowering atmospheric CO 2 concentrations, and/or increasing N supply. Successfully mitigating and adapting to declining N availability will require a broader understanding that this phenomenon is occurring alongside the more widely recognized issue of anthropogenic eutrophication. Intercalibration of isotopic records from leaves, tree rings, and lake sediments suggests that N availability in many terrestrial ecosystems has steadily declined since the beginning of the industrial era. Reductions in N availability may affect many aspects of ecosystem functioning, including carbon sequestration and herbivore nutrition. Shaded areas indicate 80% prediction intervals; marker size is proportional to the number of measurements in each annual mean. Isotope data: (tree ring) K. K. McLauchlan et al. , Sci. Rep. 7 , 7856 (2017); (lake sediment) G. W. Holtgrieve et al. , Science 334 , 1545–1548 (2011); (foliar) J. M. Craine et al. , Nat. Ecol. Evol. 2 , 1735–1744 (2018) 

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5. Evaluating population histories in Patagonia and Tierra del Fuego, Chile, using ancient mitochondrial and Y‐chromosomal DNA

   https://doi.org/10.1002/ajpa.24638  

   Balentine, Christina M. ; Alfonso‐Durruty, Marta ; Reynolds, Austin W. ; Vilar, Miguel ; Morello, Flavia ; Román, Manuel San ; Springs, Lauren C. ; Smith, Rick W. A. ; Archer, Samantha M. ; Mata‐Míguez, Jaime ; et al ( November 2022 , American Journal of Biological Anthropology)

   This study aims to characterize the genetic histories of ancient hunter‐gatherer groups in Fuego‐Patagonia (Chile) with distinct Marine, Terrestrial, and Mixed Economy subsistence strategies. Mitochondrial (mtDNA) and Y‐chromosome data were generated to test three hypotheses. H₀: All individuals were drawn from the same panmictic population; H₁: Terrestrial groups first populated the region and gave rise to highly specialized Marine groups by ~7,500 cal BP; or H₂: Marine and Terrestrial groups represent distinct ancestral lineages who migrated independently into the region.

   Ancient DNA was extracted from the teeth of 50 Fuegian‐Patagonian individuals dating from 6,895 cal BP to after European arrival, and analyzed alongside other individuals from previous studies. Individuals were assigned to Marine, Terrestrial, and Mixed Economy groups based on archeological context and stable isotope diet inferences, and mtDNA (HVR1/2) and Y‐chromosome variation was analyzed.

   Endogenous aDNA was obtained from 49/50 (98%) individuals. Haplotype diversities, F_STcomparisons, and exact tests of population differentiation showed that Marine groups were significantly different from Terrestrial groups based on mtDNA (p < 0.05). No statistically significant differences were found between Terrestrial and Mixed Economy groups. Demographic simulations support models in which Marine groups diverged from the others by ~14,000 cal BP. Y‐chromosome results showed similar patterns but were not statistically significant due to small sample sizes and allelic dropout.

   These results support the hypothesis that Marine and Terrestrial economic groups represent distinct ancestral lineages who diverged during the time populations were expanding in the Americas, and may represent independent migrations into Fuego‐Patagonia.

    

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