Elevated rates of horizontal gene transfer in the industrialized human microbiome.

Industrialization has impacted the human gut ecosystem, resulting in altered microbiome composition and diversity. Whether bacterial genomes may also adapt to the industrialization of their host populations remains largely unexplored. Here, we investigate the extent to which the rates and targets of horizontal gene transfer (HGT) vary across thousands of bacterial strains from 15 human populations spanning a range of industrialization. We show that HGTs have accumulated in the microbiome over recent host generations and that HGT occurs at high frequency within individuals. Comparison across human populations reveals that industrialized lifestyles are associated with higher HGT rates and that the functions of HGTs are related to the level of host industrialization. Our results suggest that gut bacteria continuously acquire new functionality based on host lifestyle and that high rates of HGT may be a recent development in human history linked to industrialization.

Microbial biomarkers reveal a hydrothermally active landscape at Olduvai Gorge at the dawn of the Acheulean, 1.7 Ma.

Landscape-scale reconstructions of ancient environments within the cradle of humanity may reveal insights into the relationship between early hominins and the changing resources around them. Many studies of Olduvai Gorge during Pliocene-Pleistocene times have revealed the presence of precession-driven wet-dry cycles atop a general aridification trend, though may underestimate the impact of local-scale conditions on early hominins, who likely experienced a varied and more dynamic landscape. Fossil lipid biomarkers from ancient plants and microbes encode information about their surroundings via their molecular structures and composition, and thus can shed light on past environments. Here, we employ fossil lipid biomarkers to study the paleolandscape at Olduvai Gorge at the emergence of the Acheulean technology, 1.7 Ma, through the Lower Augitic Sandstones layer. In the context of the expansion of savanna grasslands, our results represent a resource-rich mosaic ecosystem populated by groundwater-fed rivers, aquatic plants, angiosperm shrublands, and edible plants. Evidence of a geothermally active landscape is reported via an unusual biomarker distribution consistent with the presence of hydrothermal features seen today at Yellowstone National Park. The study of hydrothermalism in ancient settings and its impact on hominin evolution has not been addressed before, although the association of thermal springs in the proximity of archaeological sites documented here can also be found at other localities. The hydrothermal features and resources present at Olduvai Gorge may have allowed early hominins to thermally process edible plants and meat, supporting the possibility of a prefire stage of human evolution.

New evidence of early Neanderthal disappearance in the Iberian Peninsula.

The timing of the end of the Middle Palaeolithic and the disappearance of Neanderthals continue to be strongly debated. Current chronometric evidence from different European sites pushes the end of the Middle Palaeolithic throughout the continent back to around 42 thousand years ago (ka). This has called into question some of the dates from the Iberian Peninsula, previously considered as one of the last refuge zones of the Neanderthals. Evidence of Neanderthal occupation in Iberia after 42 ka is now very scarce and open to debate on chronological and technological grounds. Here we report thermoluminescence (TL) and optically stimulated luminescence (OSL) dates from El Salt, a Middle Palaeolithic site in Alicante, Spain, the archaeological sequence of which shows a transition from recurrent to sporadic human occupation culminating in the abandonment of the site. The new dates place this sequence within MIS 3, between ca. 60 and 45 ka. An abrupt sedimentary change towards the top of the sequence suggests a strong aridification episode coinciding with the last Neanderthal occupation of the site. These results are in agreement with current chronometric data from other sites in the Iberian Peninsula and point towards possible breakdown and disappearance of the Neanderthal local population around the time of the Heinrich 5 event. Iberian sites with recent dates (<40 ka) attributed to the Middle Palaeolithic should be revised in the light of these data.

New site at Olduvai Gorge (AGS, Bed I, 1.84 Mya) widens the range of locations where hominins engaged in butchery.

Outstanding questions about human evolution include systematic connections between critical landscape resources-such as water and food-and how these shaped the competitive and biodiverse environment(s) that our ancestors inhabited. Here, we report fossil n-alkyl lipid biomarkers and their associated δ13C values across a newly discovered Olduvai Gorge site (AGS) dated to 1.84 million years ago, enabling a multiproxy analysis of the distributions of critical local landscape resources across an explicit locus of hominin activity. Our results reveal that AGS was a seasonally waterlogged, largely unvegetated lakeside site situated near an ephemeral freshwater river surrounded by arid-adapted C4 grasses. The sparse vegetation at AGS contrasts with reconstructed (micro)habitats at the other anthropogenic sites at Olduvai Gorge, suggesting that central-provisioning places depended more heavily on water access than vegetation viz. woody plants as is often observed for modern hunter-gatherers. As hominins at AGS performed similar butchering activities as at other Bed I sites, our results suggest they did not need the shelter of trees and thus occupied a competitive position within the predatory guild.

A modern baseline for the paired isotopic analysis of skin and bone in terrestrial mammals.

We present the isotopic discrimination between paired skin and bone collagen from animals of known life history, providing a modern baseline for the interpretation of archaeological isotopic data. At present, the interpretation of inter-tissue variation (Δ(skin-bone)) in mummified remains is based on comparisons with other archaeological material, which have attributed divergence to their contrasting turnover rates, with rapidly remodelling skin collagen incorporating alterations in environmental, cultural and physiological conditions in the months prior to death. While plausible, the lack of baseline data from individuals with known life histories has hindered evaluation of the explanations presented. Our analysis of a range of animals raised under a variety of management practices showed a population-wide trend for skin collagen to be depleted in 13C by -0.7‰ and enriched in 15N by +1.0‰ relative to bone collagen, even in stillborn animals. These results are intriguing and difficult to explain using current knowledge; however, on the basis of the findings reported here, we caution any results which interpret simply on differing turnover rates. We hypothesize that there may be a consistent difference in the routing of dietary protein and lipids between skin and bone, with potentially on-site synthesis of non-essential amino acids using carbon and nitrogen that have been sourced via different biochemical pathways.

Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt.

A comprehensive view of our evolutionary history cannot ignore the ancestral features of our gut microbiota. To provide some glimpse into the past, we searched for human gut microbiome components in ancient DNA from 14 archeological sediments spanning four stratigraphic units of El Salt Middle Paleolithic site (Spain), including layers of unit X, which has yielded well-preserved Neanderthal occupation deposits dating around 50 kya. According to our findings, bacterial genera belonging to families known to be part of the modern human gut microbiome are abundantly represented only across unit X samples, showing that well-known beneficial gut commensals, such as Blautia, Dorea, Roseburia, Ruminococcus, Faecalibacterium and Bifidobacterium already populated the intestinal microbiome of Homo since as far back as the last common ancestor between humans and Neanderthals.

An Exceptionally Preserved Three-Dimensional Armored Dinosaur Reveals Insights into Coloration and Cretaceous Predator-Prey Dynamics.

Predator-prey dynamics are an important evolutionary driver of escalating predation mode and efficiency, and commensurate responses of prey [1-3]. Among these strategies, camouflage is important for visual concealment, with countershading the most universally observed [4-6]. Extant terrestrial herbivores free of significant predation pressure, due to large size or isolation, do not exhibit countershading. Modern predator-prey dynamics may not be directly applicable to those of the Mesozoic due to the dominance of very large, visually oriented theropod dinosaurs [7]. Despite thyreophoran dinosaurs' possessing extensive dermal armor, some of the most extreme examples of anti-predator structures [8, 9], little direct evidence of predation on these and other dinosaur megaherbivores has been documented. Here we describe a new, exquisitely three-dimensionally preserved nodosaurid ankylosaur, Borealopelta markmitchelli gen. et sp. nov., from the Early Cretaceous of Alberta, which preserves integumentary structures as organic layers, including continuous fields of epidermal scales and intact horn sheaths capping the body armor. We identify melanin in the organic residues through mass spectroscopic analyses and observe lighter pigmentation of the large parascapular spines, consistent with display, and a pattern of countershading across the body. With an estimated body mass exceeding 1,300 kg, B. markmitchelli was much larger than modern terrestrial mammals that either are countershaded or experience significant predation pressure as adults. Presence of countershading suggests predation pressure strong enough to select for concealment in this megaherbivore despite possession of massive dorsal and lateral armor, illustrating a significant dichotomy between Mesozoic predator-prey dynamics and those of modern terrestrial systems.

New Insights into the Evolution of the Human Diet from Faecal Biomarker Analysis in Wild Chimpanzee and Gorilla Faeces.

Our understanding of early human diets is based on reconstructed biomechanics of hominin jaws, bone and teeth isotopic data, tooth wear patterns, lithic, taphonomic and zooarchaeological data, which do not provide information about the relative amounts of different types of foods that contributed most to early human diets. Faecal biomarkers are proving to be a valuable tool in identifying relative proportions of plant and animal tissues in Palaeolithic diets. A limiting factor in the application of the faecal biomarker approach is the striking absence of data related to the occurrence of faecal biomarkers in non-human primate faeces. In this study we explored the nature and proportions of sterols and stanols excreted by our closest living relatives. This investigation reports the first faecal biomarker data for wild chimpanzee (Pan troglodytes) and mountain gorilla (Gorilla beringei). Our results suggest that the chemometric analysis of faecal biomarkers is a useful tool for distinguishing between NHP and human faecal matter, and hence, it could provide information for palaeodietary research and early human diets.

The Neanderthal meal: a new perspective using faecal biomarkers.

Neanderthal dietary reconstructions have, to date, been based on indirect evidence and may underestimate the significance of plants as a food source. While zooarchaeological and stable isotope data have conveyed an image of Neanderthals as largely carnivorous, studies on dental calculus and scattered palaeobotanical evidence suggest some degree of contribution of plants to their diet. However, both views remain plausible and there is no categorical indication of an omnivorous diet. Here we present direct evidence of Neanderthal diet using faecal biomarkers, a valuable analytical tool for identifying dietary provenance. Our gas chromatography-mass spectrometry results from El Salt (Spain), a Middle Palaeolithic site dating to ca. 50,000 yr. BP, represents the oldest positive identification of human faecal matter. We show that Neanderthals, like anatomically modern humans, have a high rate of conversion of cholesterol to coprostanol related to the presence of required bacteria in their guts. Analysis of five sediment samples from different occupation floors suggests that Neanderthals predominantly consumed meat, as indicated by high coprostanol proportions, but also had significant plant intake, as shown by the presence of 5ß-stigmastanol. This study highlights the applicability of the biomarker approach in Pleistocene contexts as a provider of direct palaeodietary information and supports the opportunity for further research into cholesterol metabolism throughout human evolution.