Facultative Carnivore Reasons

Abstract. – We provide a first checklist and review of all recognized taxa of the world’s extinct
Pleistocene and Holocene (Quaternary) turtles and tortoises that existed during the early rise
and global expansion of humanity, and most likely went extinct through a combination of earlier
hominin (e.g., Homo erectus, H. neanderthalensis) and later human (H. sapiens) exploitation, as
well as being affected by concurrent global or regional climatic and habitat changes. This checklist complements the broader listing of all modern and extant turtles and tortoises by the Turtle
Taxonomy Working Group (2014). We provide a comprehensive listing of taxonomy, names,
synonymies, and stratigraphic distribution of all chelonian taxa that have gone extinct from approximately the boundary between the Late Pliocene and Early Pleistocene, ca. 2.6 million years
ago, up through 1500 AD, at the beginning of modern times. We also provide details on modern
turtle and tortoise taxa that have gone extinct since 1500 AD. This checklist currently includes
100 fossil turtle and tortoise taxa, including 84 named and apparently distinct species, and 16 additional taxa that appear to represent additional valid species, but are only identified to genus or
family. Modern extinct turtles and tortoises include 8 species, 3 subspecies, and 1 unnamed taxon,
for 12 taxa. Of the extinct fossil taxa, terrestrial tortoises of the family Testudinidae (including
many large-bodied island forms) are the most numerous, with 60 taxa. When the numbers for
fossil tortoises are combined with the 61 modern (living and extinct) species of tortoises, of the 121
tortoise species that have existed at some point since the beginning of the Pleistocene, 69 (57.0%)
have gone extinct. This likely reflects the high vulnerability of these large and slow terrestrial (often
insular) species primarily to human exploitation. The other large-bodied terrestrial turtles, the giant horned turtles of the family Meiolaniidae, with 7 taxa (also often insular), all went extinct
by the Late Holocene while also exploited by humans. The total global diversity of turtles and
tortoises that has existed during the history of hominin utilization of chelonians, and that are
currently recognized as distinct and included on our two checklists, consists of 336 modern species and 100 extinct Pleistocene and Holocene taxa, for a total of 436 chelonian species. Of these,
109 species (25.0%) and 112 total taxa are estimated to have gone extinct since the beginning of
the Pleistocene. The chelonian diversity and its patterns of extinctions during the Quaternary
inform our understanding of the impacts of the history of human exploitation of turtles and the
effects of climate change, and their relevance to current and future patterns.

Key Words. – Reptilia, Testudines, turtle, tortoise, chelonian, taxonomy, distribution, extinction,
fossils, paleontology, archaeology, humanity, hominin, exploitation, chelonophagy, megafauna,
island refugia, climate change, Pliocene, Pleistocene, Holocene, Anthropocene, Quaternary

The human trophic level (HTL) during the Pleistocene and its degree of variability serve, explicitly or tacitly, as the basis of many explanations for human evolution, behavior, and culture. Previous attempts to reconstruct the HTL have relied heavily on an analogy with recent hunter-gatherer groups' diets. In addition to technological differences, recent findings of substantial ecological differences between the Pleistocene and the Anthropocene cast doubt regarding that analogy's validity. Surprisingly little systematic evolution-guided evidence served to reconstruct HTL. Here, we reconstruct the HTL during the Pleistocene by reviewing evidence for the impact of the HTL on the biological, ecological, and behavioral systems derived from various existing studies. We adapt a paleobiological and paleoecological approach, including evidence from human physiology and genetics, archaeology, paleontology, and zoology, and identified 25 sources of evidence in total. The evidence shows that the trophic level of the Homo lineage that most probably led to modern humans evolved from a low base to a high, carnivorous position during the Pleistocene, beginning with Homo habilis and peaking in Homo erectus. A reversal of that trend appears in the Upper Paleolithic, strengthening in the Mesolithic/Epipaleolithic and Neolithic, and culminating with the advent of agriculture. We conclude that it is possible to reach a credible reconstruction of the HTL without relying on a simple analogy with recent hunter-gatherers' diets. The memory of an adaptation to a trophic level that is embedded in modern humans' biology in the form of genetics, metabolism, and morphology is a fruitful line of investigation of past HTLs, whose potential we have only started to explore.

There is a broad consensus in nutritional-microbiota research that high-fat (HF) diets are harmful to human health, at least in part through their modulation of the gut microbiota. However, various studies also support the inherent flexibility of the human gut and our microbiota’s ability to adapt to a variety of food sources, suggesting a more nuanced picture. In this article, we first discuss some problems facing basic translational research and provide a different framework for thinking about diet and gut health in terms of metabolic flexibility. We then offer evidence that well-formulated HF diets, such as ketogenic diets, may provide healthful alternative fuel sources for the human gut. We place this in the context of cancer research, where this concern over HF diets is also expressed, and consider various potential objections concerning the effects of lipopolysaccharides, trimethylamine-N-oxide, and secondary bile acids on human gut health. We end by providing some general suggestions for how to improve research and clinical practice with respect to the gut microbiota when considering the framework of metabolic flexibility.

Helicobacter pylori disturbs the stomach lining during long-term colonization of its human host, with sequelae including ulcers and gastric cancer1,2. Numerous H. pylori virulence factors have been identified, showing extensive geographic variation1. Here we identify a ‘Hardy’ ecospecies of H. pylori that shares the ancestry of ‘Ubiquitous’ H. pylori from the same region in most of the genome but has nearly fixed single-nucleotide polymorphism differences in 100 genes, many of which encode outer membrane proteins and host interaction factors. Most Hardy strains have a second urease, which uses iron as a cofactor rather than nickel3, and two additional copies of the vacuolating cytotoxin VacA. Hardy strains currently have a limited distribution, including in Indigenous populations in Siberia and the Americas and in lineages that have jumped from humans to other mammals. Analysis of polymorphism data implies that Hardy and Ubiquitous coexisted in the stomachs of modern humans since before we left Africa and that both were dispersed around the world by our migrations. Our results also show that highly distinct adaptive strategies can arise and be maintained stably within bacterial populations, even in the presence of continuous genetic exchange between strains.

The purpose of this article is to reconcile the hypotheses that: (1) brain evolution occurred due to a change in diet, and (2) it occurred due to pressures related to understanding more and more about the underlying causes, such as understanding increasingly complex manipulative and cooperative intentions on the part of the other, as well as understanding reality itself (and how to interact with it beyond group issues). I argue that the ingestion of fat, a highly energy-efficient food, would have unlocked the evolutionary process that culminated in the emergence of the practice of reasoning about underlying causes; and that the consolidation of such a practice resulted in a continuous pressure to increase cognition about “whys”; so that many explanations ended up imposing the need for additional ones, and with that came a high level of awareness and the need for the brain to evolve not only in terms of providing a higher level of cognition but also in size.

Saturated fat: villain and bogeyman in the development of cardiovascular disease?

Abstract
Background
Cardiovascular disease (CVD) is the leading global cause of death. For decades, the conventional wisdom has been that the consumption of saturated fat (SFA) undermines cardiovascular health, clogs the arteries, increases risk of CVD and leads to heart attacks. It is timely to investigate whether this claim holds up to scientific scrutiny.

Objectives
The purpose of this paper is to review and discuss recent scientific evidence on the association between dietary SFA and CVD.

Methods
PubMed, Google scholar and Scopus were searched for articles published between 2010 and 2021 on the association between SFA consumption and CVD risk and outcomes. A review was conducted examining observational studies and prospective epidemiologic cohort studies, RCTs, systematic reviews and meta analyses of observational studies and prospective epidemiologic cohort studies and long-term RCTs.

Results
Collectively, neither observational studies, prospective epidemiologic cohort studies, RCTs, systematic reviews and meta analyses have conclusively established a significant association between SFA in the diet and subsequent cardiovascular risk and CAD, MI or mortality nor a benefit of reducing dietary SFAs on CVD rick, events and mortality. Beneficial effects of replacement of SFA by polyunsaturated or monounsaturated fat or carbohydrates remain elusive.

Conclusions
Findings from the studies reviewed in this paper indicate that the consumption of SFA is not significantly associated with CVD risk, events or mortality. Based on the scientific evidence, there is no scientific ground to demonize SFA as a cause of CVD. SFA naturally occurring in nutrient-dense foods can be safely included in the diet.

Humans are unique in their diet, physiology and socio-reproductive behavior compared to other primates. They are also unique in the ubiquitous adaptation to all biomes and habitats. From an evolutionary perspective, these trends seem to have started about two million years ago, coinciding with the emergence of encephalization, the reduction of the dental apparatus, the adoption of a fully terrestrial lifestyle, resulting in the emergence of the modern anatomical bauplan, the focalization of certain activities in the landscape, the use of stone tools, and the exit from Africa. It is in this period that clear taphonomic evidence of a switch in diet with respect to Pliocene hominins occurred, with the adoption of carnivory. Until now, the degree of carnivorism in early humans remained controversial. A persistent hypothesis is that hominins acquired meat irregularly (potentially as fallback food) and opportunistically through klepto-foraging. Here, we test this hypothesis and show, in contrast, that the butchery practices of early Pleistocene hominins (unveiled through systematic study of the patterning and intensity of cut marks on their prey) could not have resulted from having frequent secondary access to carcasses. We provide evidence of hominin primary access to animal resources and emphasize the role that meat played in their diets, their ecology and their anatomical evolution, ultimately resulting in the ecologically unrestricted terrestrial adaptation of our species. This has major implications to the evolution of human physiology and potentially for the evolution of the human brain.

Phylogenetic rate shifts in feeding time during the evolution of Homo

Unique among animals, humans eat a diet rich in cooked and nonthermally processed food. The ancestors of modern humans who invented food processing (including cooking) gained critical advantages in survival and fitness through increased caloric intake. However, the time and manner in which food processing became biologically significant are uncertain. Here, we assess the inferred evolutionary consequences of food processing in the human lineage by applying a Bayesian phylogenetic outlier test to a comparative dataset of feeding time in humans and nonhuman primates. We find that modern humans spend an order of magnitude less time feeding than predicted by phylogeny and body mass (4.7% vs. predicted 48% of daily activity). This result suggests that a substantial evolutionary rate change in feeding time occurred along the human branch after the human–chimpanzee split. Along this same branch, Homo erectus shows a marked reduction in molar size that is followed by a gradual, although erratic, decline in H. sapiens. We show that reduction in molar size in early Homo (H. habilis and H. rudolfensis) is explicable by phylogeny and body size alone. By contrast, the change in molar size to H. erectus, H. neanderthalensis, and H. sapiens cannot be explained by the rate of craniodental and body size evolution. Together, our results indicate that the behaviorally driven adaptations of food processing (reduced feeding time and molar size) originated after the evolution of Homo but before or concurrent with the evolution of H. erectus, which was around 1.9 Mya.

Diet and the evolution of the earliest human ancestors

Over the past decade, discussions of the evolution of the earliest human ancestors have focused on the locomotion of the australopithecines. Recent discoveries in a broad range of disciplines have raised important questions about the influence of ecological factors in early human evolution. Here we trace the cranial and dental traits of the early australopithecines through time, to show that between 4.4 million and 2.3 million years ago, the dietary capabilities of the earliest hominids changed dramatically, leaving them well suited for life in a variety of habitats and able to cope with significant changes in resource availability associated with long-term and short-term climatic fluctuations.

Impact of meat and Lower Palaeolithic food processing techniques on chewing in humans

The origins of the genus Homo are murky, but by H. erectus, bigger brains and bodies had evolved that, along with larger foraging ranges, would have increased the daily energetic requirements of hominins1,2. Yet H. erectus differs from earlier hominins in having relatively smaller teeth, reduced chewing muscles, weaker maximum bite force capabilities, and a relatively smaller gut3,4,5. This paradoxical combination of increased energy demands along with decreased masticatory and digestive capacities is hypothesized to have been made possible by adding meat to the diet6,7,8, by mechanically processing food using stone tools7,9,10, or by cooking11,12. Cooking, however, was apparently uncommon until 500,000 years ago13,14, and the effects of carnivory and Palaeolithic processing techniques on mastication are unknown. Here we report experiments that tested how Lower Palaeolithic processing technologies affect chewing force production and efficacy in humans consuming meat and underground storage organs (USOs). We find that if meat comprised one-third of the diet, the number of chewing cycles per year would have declined by nearly 2 million (a 13% reduction) and total masticatory force required would have declined by 15%. Furthermore, by simply slicing meat and pounding USOs, hominins would have improved their ability to chew meat into smaller particles by 41%, reduced the number of chews per year by another 5%, and decreased masticatory force requirements by an additional 12%. Although cooking has important benefits, it appears that selection for smaller masticatory features in Homo would have been initially made possible by the combination of using stone tools and eating meat.

Many mammals run faster and for longer than humans and have superior cardiovascular physiologies. Yet humans are considered by some scholars to be excellent endurance runners at high ambient temperatures, and in our past to have been persistence hunters capable of running down fleeter quarry over extended periods during the heat of the day. This suggests that human endurance running is less affected by high ambient temperatures than is that of other cursorial ungulates. However, there are no investigations of this hypothesis. We took advantage of longitudinal race results available for three annual events that pit human athletes directly against a hyper-adapted ungulate racer, the thoroughbred horse. Regressing running speed against ambient temperature shows race speed deteriorating with hotter temperatures more slowly in humans than in horses. This is the first direct evidence that human running is less inhibited by high ambient temperatures than that of another endurance species, supporting the argument that we are indeed adapted for high temperature endurance running. Nonetheless, it is far from clear that this capacity is explained by an endurance hunting past because in absolute terms humans are slower than horses and indeed many other ungulate species. While some human populations have persistence hunted (and on occasion still do), the success of this unlikely foraging strategy may be best explained by the application of another adaption – high cognitive capacity. With dedication, experience and discipline, capitalising on their small endurance advantage in high temperatures, humans have a chance of running a more athletic prey to exhaustion.

Compared to other primates, humans are exceptional long-distance runners, a feature that emerged in genus Homo approximately 2 Ma and is classically attributed to anatomical and physiological adaptations such as an enlarged gluteus maximus and improved heat dissipation. However, no underlying genetic changes have currently been defined. Two to three million years ago, an exon deletion in the CMP-Neu5Ac hydroxylase (CMAH) gene also became fixed in our ancestral lineage. Cmah loss in mice exacerbates disease severity in multiple mouse models for muscular dystrophy, a finding only partially attributed to differences in immune reactivity. We evaluated the exercise capacity of Cmah−/− mice and observed an increased performance during forced treadmill testing and after 15 days of voluntary wheel running. Cmah−/− hindlimb muscle exhibited more capillaries and a greater fatigue resistance in situ. Maximal coupled respiration was also higher in Cmah null mice ex vivo and relevant differences in metabolic pathways were also noted. Taken together, these data suggest that CMAH loss contributes to an improved skeletal muscle capacity for oxygen use. If translatable to humans, CMAH loss could have provided a selective advantage for ancestral Homo during the transition from forest dwelling to increased resource exploration and hunter/gatherer behaviour in the open savannah.

Significance
Human lifestyles profoundly influence the communities of microorganisms that inhabit the body, that is, the microbiome; however, how the microbiomes of humans have diverged from those found within wild-living hominids is not clear. To establish how the gut microbiome has changed since the diversification of human and ape species, we characterized the microbial assemblages residing within hundreds of wild chimpanzees, bonobos, and gorillas. Changes in the composition of the microbiome accrued steadily as African apes diversified, but human microbiomes have diverged at an accelerated pace owing to a dramatic loss of ancestral microbial diversity. These results suggest that the human microbiome has undergone a substantial transformation since the human–chimpanzee split.
Abstract
Humans are ecosystems containing trillions of microorganisms, but the evolutionary history of this microbiome is obscured by a lack of knowledge about microbiomes of African apes. We sequenced the gut communities of hundreds of chimpanzees, bonobos, and gorillas and developed a phylogenetic approach to reconstruct how present-day human microbiomes have diverged from those of ancestral populations. Compositional change in the microbiome was slow and clock-like during African ape diversification, but human microbiomes have deviated from the ancestral state at an accelerated rate. Relative to the microbiomes of wild apes, human microbiomes have lost ancestral microbial diversity while becoming specialized for animal-based diets. Individual wild apes cultivate more phyla, classes, orders, families, genera, and species of bacteria than do individual humans across a range of societies. These results indicate that humanity has experienced a depletion of the gut flora since diverging from Pan.