Nuku, a family of primate retrocopies derived from KU70

The ubiquitous DNA repair protein, Ku70p, has undergone extensive copy number expansion during primate evolution. Gene duplications of KU70 have the hallmark of long interspersed element-1 mediated retrotransposition with evidence of target-site duplications, the poly-A tails, and the absence of introns. Evolutionary analysis of this expanded family of KU70-derived “NUKU” retrocopies reveals that these genes are both ancient and also actively being created in extant primate species. NUKU retrocopies show evidence of functional divergence away from KU70, as evinced by their altered pattern of tissue expression and possible tissue specific translation. Molecular modeling predicted that amino acid changes in Nuku2p at the interaction interface with Ku80p would prevent the assembly of the Ku heterodimer. The lack of Nuku2p-Ku80p interaction was confirmed by yeast two-hybrid assay, which contrasts the robust interaction of Ku70p-Ku80p. While several NUKU retrocopies appear to have been degraded by mutation, NUKU2 shows evidence of positive natural selection, suggesting that this retrocopy is undergoing neofunctionalization. Although Nuku proteins do not appear to antagonize retrovirus transduction in cell culture, the observed expansion and rapid evolution of NUKUs could be being driven by alternative selective pressures related to infectious disease or an undefined role in primate physiology.

Tooth chipping patterns in Paranthropus do not support regular hard food mastication

The paranthropines, including Paranthropus boisei and Paranthropus robustus, have often been considered hard-food specialists. The large post-canine teeth, thick enamel, and robust craniofacial features are often suggested to have evolved to cope with habitual mastication of hard foods. Yet, direct evidence for Paranthropus feeding behaviour often challenges these morphological interpretations. The main exception being antemortem tooth chipping which is still regularly used as evidence of habitual mastication of hard foods in this genus. In this study, data were compiled from the literature for six hominin species (including P. boisei and P. robustus) and 17 extant primate species, to analyse Paranthropus chipping patterns in a broad comparative framework. Severity of fractures, position on the dentition, and overall prevalence were compared among species. The results indicate that both Paranthropus species had a lower prevalence of tooth fractures compared to other fossil hominin species (P. boisei: 4%; P. robustus: 11%; Homo naledi: 37%; Australopithecus africanus: 17%; Homo neanderthalensis: 45%; Epipalaeolithic Homo sapiens: 29%); instead, their frequencies are similar to apes that masticate hard items in a non-regular frequency, including chimpanzees, gibbons, and gorillas (4%, 7% and 9% respectively). The prevalence is several times lower than in extant primates known to habitually consume hard items, such as sakis, mandrills, and sooty mangabeys (ranging from 28% to 48%). Comparative chipping analysis suggests that both Paranthropus species were unlikely habitual hard object eaters, at least compared to living durophage analogues.

Nuku, a family of primate retrogenes derived from KU70

The ubiquitous DNA repair protein, Ku70p, has undergone extensive copy number expansion during primate evolution. Gene duplications of KU70 have the hallmark of long interspersed element-1 (LINE-1) mediated retrotransposition with evidence of target-site duplications, the poly-A tails, and the absence of introns. Evolutionary analysis of this expanded family of KU70-derived “NUKU” retrogenes reveals that these genes are both ancient and also actively being created in extant primate species. NUKU retrogenes show evidence of functional divergence away from KU70, as evinced by their altered pattern of tissue expression and possible translation in the human testes. Molecular modeling predicted that mutations in Nuku2p at the interaction interface with Ku80p would prevent the assembly of the Ku heterodimer. The lack of Nuku2p-Ku80p interaction was confirmed by yeast two-hybrid assay, which contrasts the robust interaction of Ku70p-Ku80p. While several NUKU retrogenes appear to have been degraded by mutation, NUKU2 shows evidence of positive natural selection, suggesting that this retrogene is undergoing neofunctionalization. Although Nuku proteins do not appear to antagonize retroviruses in cell culture, the observed expansion and rapid evolution of NUKUs could be being driven by alternative selective pressures related to infectious disease or an undefined role in primate physiology.

Current and future trends in socio-economic, demographic and governance factors affecting global primate conservation

Currently, ~65% of extant primate species (ca 512 species) distributed in 91 countries in the Neotropics, mainland Africa, Madagascar, South Asia and Southeast Asia are threatened with extinction and 75% have declining populations as a result of deforestation and habitat loss resulting from increasing global market demands, and land conversion for industrial agriculture, cattle production and natural resource extraction. Other pressures that negatively impact primates are unsustainable bushmeat hunting, the illegal trade of primates as pets and as body parts, expanding road networks in previously isolated areas, zoonotic disease transmission and climate change. Here we examine current and future trends in several socio-economic factors directly or indirectly affecting primates to further our understanding of the interdependent relationship between human well-being, sustainable development, and primate population persistence. We found that between 2001 and 2018 ca 191 Mha of tropical forest (30% canopy cover) were lost as a result of human activities in the five primate range regions. Forty-six percent of this loss was in the Neotropics (Mexico, Central and South America), 30% in Southeast Asia, 21% in mainland Africa, 2% in Madagascar and 1% in South Asia. Countries with the greatest losses (ca 57% of total tree cover loss) were Brazil, Indonesia, DRC, China, and Malaysia. Together these countries harbor almost 50% of all extant primate species. In 2018, the world human population was estimated at ca 8bn people, ca 60% of which were found in primate range countries. Projections to 2050 and to 2100 indicate continued rapid growth of the human populations in these five primate range regions, with Africa surpassing all the other regions and totaling ca 4bn people by the year 2100. Socioeconomic indicators show that, compared to developed nations, most primate range countries are characterized by high levels of poverty and income inequality, low human development, low food security, high levels of corruption and weak governance. Models of Shared Socioeconomic Pathway scenarios (SSPs) projected to 2050 and 2100 showed that whereas practices of increasing inequality (SSP4) or unconstrained growth in economic output and energy use (SSP5) are projected to have dire consequences for human well-being and primate survivorship, practices of sustainability-focused growth and equality (SSP1) are expected to have a positive effect on maintaining biodiversity, protecting environments, and improving the human condition. These results stress that improving the well-being, health, and security of the current and future human populations in primate range countries are of paramount importance if we are to move forward with effective policies to protect the world’s primate species and promote biodiversity conservation.

Daily Distance Traveled Is Associated with Greater Brain Size in Primates

Explanations for the brain size increments through primate and, particularly, human evolution are numerous. Commonly, these hypotheses rely on the influence that behavioral and ecological variables have on brain size in extant primates, such as diet quality, social group size, or home range (HR) area. However, HR area does not reflect the time spent moving. As such, it has not been properly addressed whether the effort involved in movement could have affected brain size evolution in primates. This study aimed to test the influence of daily movement on primates’ brain sizes, controlling for these other behavioral and ecological factors. We used a large comparative dataset of extant primate species and phylogenetic comparative methods. Our results show a significant correlation between daily movement and brain mass, which is not explained by the influence of diet, social group size, HR, or body mass. Hence, from an evolutionary timescale, a longer daily movement distance is not a constraining factor for the energetic investment in a larger brain. On the contrary, increased mobility could have contributed to brain mass incrementations through evolution.

Evidence in hand: recent discoveries and the early evolution of human manual manipulation

For several decades, it was largely assumed that stone tool use and production were abilities limited to the genus Homo . However, growing palaeontological and archaeological evidence, comparative extant primate studies, as well as results from methodological advancements in biomechanics and morphological analyses, have been gradually accumulating and now provide strong support for more advanced manual manipulative abilities and tool-related behaviours in pre- Homo hominins than has been traditionally recognized. Here, I review the fossil evidence related to early hominin dexterity, including the recent discoveries of relatively complete early hominin hand skeletons, and new methodologies that are providing a more holistic interpretation of hand function, and insight into how our early ancestors may have balanced the functional requirements of both arboreal locomotion and tool-related behaviours.

Dietary quality and encephalization in platyrrhine primates

The high energetic costs of building and maintaining large brains are thought to constrain encephalization. The ‘expensive-tissue hypothesis’ (ETH) proposes that primates (especially humans) overcame this constraint through reduction of another metabolically expensive tissue, the gastrointestinal tract. Small guts characterize animals specializing on easily digestible diets. Thus, the hypothesis may be tested via the relationship between brain size and diet quality. Platyrrhine primates present an interesting test case, as they are more variably encephalized than other extant primate clades (excluding Hominoidea). We find a high degree of phylogenetic signal in the data for diet quality, endocranial volume and body size. Controlling for phylogenetic effects, we find no significant correlation between relative diet quality and relative endocranial volume. Thus, diet quality fails to account for differences in platyrrhine encephalization. One taxon, in particular, Brachyteles , violates predictions made by ETH in having a large brain and low-quality diet. Dietary reconstructions of stem platyrrhines further indicate that a relatively high-quality diet was probably in place prior to increases in encephalization. Therefore, it is unlikely that a shift in diet quality was a primary constraint release for encephalization in platyrrhines and, by extrapolation, humans.

Molar microwear textures and the diets of Australopithecus anamensis and Australopithecus afarensis

Many researchers have suggested that Australopithecus anamensis and Australopithecus afarensis were among the earliest hominins to have diets that included hard, brittle items. Here we examine dental microwear textures of these hominins for evidence of this. The molars of three Au. anamensis and 19 Au. afarensis specimens examined preserve unobscured antemortem microwear. Microwear textures of these individuals closely resemble those of Paranthropus boisei , having lower complexity values than Australopithecus africanus and especially Paranthropus robustus . The microwear texture complexity values for Au. anamensis and Au. afarensis are similar to those of the grass-eating Theropithecus gelada and folivorous Alouatta palliata and Trachypithecus cristatus . This implies that these Au. anamensis and Au. afarensis individuals did not have diets dominated by hard, brittle foods shortly before their deaths. On the other hand, microwear texture anisotropy values for these taxa are lower on average than those of Theropithecus , Alouatta or Trachypithecus . This suggests that the fossil taxa did not have diets dominated by tough foods either, or if they did that directions of tooth–tooth movement were less constrained than in higher cusped and sharper crested extant primate grass eaters and folivores.