Secondary structure construction and molecular identification of rRNA 18S V4 region E23-5-E23-6 of parasitic lice of Hominidae.

The parasitic lice of Hominidae are a class of blood-sucking insects, having a large fragment expansion region in ribosome 18S V4 region. In this study, the value of the E23-5-E23-6 stem-loop structure in the insertion region for molecular identification of lice were explored through motif analysis and secondary structure construction. Five pubic lice samples from China were morphologically identified, and primers for the rRNA 18S V4 region were designed for molecular identification. The V4 sequence of the parasitic lice of Hominidae was retrieved from GenBank for sequence analysis. The five samples were identified as pubic lice based on V4 region, which were of the same specie but geographically different from Australian strains in Genbank, with the identity of 99.06-99.46%. Compared with the human lice, both the chimpanzee lice and pubic lice had large indel fragments in the V4 region. Comparison results showed that Muscle and MAFFT had better alignment and phylogeny results than Clustal. The large expansion region, comprising E23-5 and E23-6, was located between E23-4 and E23-7. The V4 secondary structure showed that the stem-loop structures of the lice parasitizing on pubic area, human, and chimpanzee were different in the E23-5 and E23-6, which could effectively distinguish the three parasitic lice and divide the human lice into five genotypes. This is suitable not only for the identification of three lice species in higher taxonomic ranks but also for genotype identification of human lice in lower taxonomic ranks. The difference between the stem-loop structure is more intuitive than that between the primary sequences.

Phylogenetic analysis of Middle-Late Miocene apes.

Despite intensive study, many aspects of the evolutionary history of great apes and humans (Hominidae) are not well understood. In particular, the phylogenetic relationships of many fossil taxa remain poorly resolved. This study aims to provide an updated hypothesis of phylogenetic relationships for Middle-Late Miocene fossil apes, focusing on those taxa typically considered to be great apes. The character matrix compiled here samples 274 characters from the skull, dentition, and postcranium. Multiple iterations were performed to examine the effects of ingroup taxon selection, outgroup constraints, treatment of continuous data, character partitions (craniodental, postcranial), and missing data. Parsimony and Bayesian methods were used to infer phylogenetic relationships. Most European hominoids (Hispanopithecus, Rudapithecus, Dryopithecus, Pierolapithecus) are recovered as stem hominids, not more closely related to orangutans or to African apes and humans (Homininae), whereas Ouranopithecus, Graecopithecus, and Nakalipithecus are inferred to be members of the hominine clade. Asian fossil hominoids, with the exception of Lufengpithecus hudienensis, are recovered as part of the orangutan clade (Ponginae). Results suggest that Kenyapithecus and Griphopithecus are possible stem hominids, whereas Equatorius and Nacholapithecus are consistently recovered as stem hominoids. Oreopithecus and Samburupithecus are not recovered as hominids. Results of Bayesian analyses differ from those of parsimony analyses. Craniodental and postcranial character partitions are incongruent in the placement of hylobatids, which is interpreted as evidence that hylobatids and hominids independently evolved adaptations to suspensory positional behaviors. An understanding of phylogenetic relationships is necessary to address many of the questions asked in paleoanthropology. Thus, the updated hypothesis of phylogenetic relationships presented here can be used to gain a better understanding of important morphological transitions that took place during hominid evolution, ancestral morphotypes at key nodes, and the biogeography of the clade.

Social pressure drives "conversational rules" in great apes.

In the last decade, two hypotheses, one on the evolution of animal vocal communication in general and the other on the origins of human language, have gained ground. The first hypothesis argues that the complexity of communication co-evolved with the complexity of sociality. Species forming larger groups with complex social networks have more elaborate vocal repertoires. The second hypothesis posits that the core of communication is represented not only by what can be expressed by an isolated caller, but also by the way that vocal interactions are structured, language being above all a social act. Primitive forms of conversational rules based on a vocal turn-taking principle are thought to exist in primates. To support and bring together these hypotheses, more comparative studies of socially diverse species at different levels of the primate phylogeny are needed. However, the majority of available studies focus on monkeys, primates that are distant from the human lineage. Great apes represent excellent candidates for such comparative studies because of their phylogenetic proximity to humans and their varied social lives. We propose that studying vocal turn-taking in apes could address several major gaps regarding the social relevance of vocal turn-taking and the evolutionary trajectory of this behaviour among anthropoids. Indeed, how the social structure of a species may influence the vocal interaction patterns observed among group members remains an open question. We gathered data from the literature as well as original unpublished data (where absent in the literature) on four great ape species: chimpanzees Pan troglodytes, bonobos Pan paniscus, western lowland gorillas Gorilla gorilla gorilla and Bornean orang-utans Pongo pygmaeus. We found no clear-cut relationship between classical social complexity metrics (e.g. number of group members, interaction rates) and vocal complexity parameters (e.g. repertoire size, call rates). Nevertheless, the nature of the society (i.e. group composition, diversity and valence of social bonds) and the type of vocal interaction patterns (isolated calling, call overlap, turn-taking-based vocal exchanges) do appear to be related. Isolated calling is the main vocal pattern found in the species with the smallest social networks (orang-utan), while the other species show vocal interactions that are structured according to temporal rules. A high proportion of overlapping vocalisations is found in the most competitive species (chimpanzee), while vocal turn-taking predominates in more tolerant bonobos and gorillas. Also, preferentially interacting individuals and call types used to interact are not randomly distributed. Vocal overlap ('chorusing') and vocal exchange ('conversing') appear as possible social strategies used to advertise/strengthen social bonds. Our analyses highlight that: (i) vocal turn-taking is also observed in non-human great apes, revealing universal rules for conversing that may be deeply rooted in the primate lineage; (ii) vocal interaction patterns match the species' social lifestyle; (iii) although limited to four species here, adopting a targeted comparative approach could help to identify the multiple and subtle factors underlying social and vocal complexity. We believe that vocal interaction patterns form the basis of a promising field of investigation that may ultimately improve our understanding of the socially driven evolution of communication.

Apes in fiction: does the content of novels reflect primatological knowledge?

Novels about great apes and humans continue to be consistently popular with the reading public, sometimes reaching best-seller status. Media reviews of these books rarely comment on their primatological roots, nor do primatological journals review them. In a non-quantitative, pilot study, I scrutinize six prominent novels, in terms of three questions: How do the novels make use of primatology? What aspects of primatology do they use? How accurate is their use of primatology? Such novels overwhelmingly concentrate on language, with intelligence and sexuality lagging far behind; other topics, such as culture or technology, receive little or no attention. Apes in nature are rarely mentioned. Inaccuracies abound, even at the most basic level of primatological knowledge that easily could be remedied. Both authors and primatologists would benefit from more informative interaction before publication.

Reassessment of the phylogenetic relationships of the late Miocene apes Hispanopithecus and Rudapithecus based on vestibular morphology.

Late Miocene great apes are key to reconstructing the ancestral morphotype from which earliest hominins evolved. Despite consensus that the late Miocene dryopith great apes Hispanopithecus laietanus (Spain) and Rudapithecus hungaricus (Hungary) are closely related (Hominidae), ongoing debate on their phylogenetic relationships with extant apes (stem hominids, hominines, or pongines) complicates our understanding of great ape and human evolution. To clarify this question, we rely on the morphology of the inner ear semicircular canals, which has been shown to be phylogenetically informative. Based on microcomputed tomography scans, we describe the vestibular morphology of Hispanopithecus and Rudapithecus, and compare them with extant hominoids using landmark-free deformation-based three-dimensional geometric morphometric analyses. We also provide critical evidence about the evolutionary patterns of the vestibular apparatus in living and fossil hominoids under different phylogenetic assumptions for dryopiths. Our results are consistent with the distinction of Rudapithecus and Hispanopithecus at the genus rank, and further support their allocation to the Hominidae based on their derived semicircular canal volumetric proportions. Compared with extant hominids, the vestibular morphology of Hispanopithecus and Rudapithecus most closely resembles that of African apes, and differs from the derived condition of orangutans. However, the vestibular morphologies reconstructed for the last common ancestors of dryopiths, crown hominines, and crown hominids are very similar, indicating that hominines are plesiomorphic in this regard. Therefore, our results do not conclusively favor a hominine or stem hominid status for the investigated dryopiths.

Sexual dimorphism in human arm power and force: implications for sexual selection on fighting ability.

Sexual dimorphism often arises from selection on specific musculoskeletal traits that improve male fighting performance. In humans, one common form of fighting includes using the fists as weapons. Here, we tested the hypothesis that selection on male fighting performance has led to the evolution of sexual dimorphism in the musculoskeletal system that powers striking with a fist. We compared male and female arm cranking power output, using it as a proxy for the power production component of striking with a fist. Using backward arm cranking as an unselected control, our results indicate the presence of pronounced male-biased sexual dimorphism in muscle performance for protracting the arm to propel the fist forward. We also compared overhead pulling force between males and females, to test the alternative hypothesis that sexual dimorphism in the upper body of humans is a result of selection on male overhead throwing ability. We found weaker support for this hypothesis, with less pronounced sexual dimorphism in overhead arm pulling force. The results of this study add to a set of recently identified characters indicating that sexual selection on male aggressive performance has played a role in the evolution of the human musculoskeletal system and the evolution of sexual dimorphism in hominins.

LIMK2-1 is a Hominidae-Specific Isoform of LIMK2 Expressed in Central Nervous System and Associated with Intellectual Disability.

LIMK2 is involved in neuronal functions by regulating actin dynamics. Different isoforms of LIMK2 are described in databanks. LIMK2a and LIMK2b are the most characterized. A few pieces of evidence suggest that LIMK2 isoforms might not have overlapping functions. In this study, we focused our attention on a less studied human LIMK2 isoform, LIMK2-1. Compared to the other LIMK2 isoforms, LIMK2-1 contains a supplementary C-terminal phosphatase 1 inhibitory domain (PP1i). We found out that this isoform was hominidae-specific and showed that it was expressed in human fetal brain and faintly in adult brain. Its coding sequence was sequenced in 173 patients with sporadic non-syndromic intellectual disability (ID), and we observed an association of a rare missense variant in the PP1i domain (rs151191437, p.S668P) with ID. Our results also suggest an implication of LIMK2-1 in neurite outgrowth and neurons arborization which appears to be affected by the p.S668P variation. Therefore our results suggest that LIMK2-1 plays a role in the developing brain, and that a rare variation of this isoform is a susceptibility factor in ID.

Recent evolution of the human skin barrier.

The skin is the first line of defense against the environment, with the epidermis as the outermost tissue providing much of the barrier function. Given its direct exposure to and encounters with the environment, the epidermis must evolve to provide an optimal barrier for the survival of an organism. Recent advances in genomics have identified a number of genes for the human skin barrier that have undergone evolutionary changes since humans diverged from chimpanzees. Here, we highlight a selection of key and innovative genetic findings for skin barrier evolution in our divergence from our primate ancestors and among modern human populations.

Elucidation of cross-species proteomic effects in human and hominin bone proteome identification through a bioinformatics experiment.

BACKGROUND: The study of ancient protein sequences is increasingly focused on the analysis of older samples, including those of ancient hominins. The analysis of such ancient proteomes thereby potentially suffers from "cross-species proteomic effects": the loss of peptide and protein identifications at increased evolutionary distances due to a larger number of protein sequence differences between the database sequence and the analyzed organism. Error-tolerant proteomic search algorithms should theoretically overcome this problem at both the peptide and protein level; however, this has not been demonstrated. If error-tolerant searches do not overcome the cross-species proteomic issue then there might be inherent biases in the identified proteomes. Here, a bioinformatics experiment is performed to test this using a set of modern human bone proteomes and three independent searches against sequence databases at increasing evolutionary distances: the human (0 Ma), chimpanzee (6-8 Ma) and orangutan (16-17 Ma) reference proteomes, respectively. RESULTS: Incorrectly suggested amino acid substitutions are absent when employing adequate filtering criteria for mutable Peptide Spectrum Matches (PSMs), but roughly half of the mutable PSMs were not recovered. As a result, peptide and protein identification rates are higher in error-tolerant mode compared to non-error-tolerant searches but did not recover protein identifications completely. Data indicates that peptide length and the number of mutations between the target and database sequences are the main factors influencing mutable PSM identification. CONCLUSIONS: The error-tolerant results suggest that the cross-species proteomics problem is not overcome at increasing evolutionary distances, even at the protein level. Peptide and protein loss has the potential to significantly impact divergence dating and proteome comparisons when using ancient samples as there is a bias towards the identification of conserved sequences and proteins. Effects are minimized between moderately divergent proteomes, as indicated by almost complete recovery of informative positions in the search against the chimpanzee proteome (≈90%, 6-8 Ma). This provides a bioinformatic background to future phylogenetic and proteomic analysis of ancient hominin proteomes, including the future description of novel hominin amino acid sequences, but also has negative implications for the study of fast-evolving proteins in hominins, non-hominin animals, and ancient bacterial proteins in evolutionary contexts.

Pathogen Transmission from Humans to Great Apes is a Growing Threat to Primate Conservation.

All six great ape species are listed as endangered or critically endangered by the IUCN and experiencing decreasing population trends. One of the threats to these non-human primates is the transmission of pathogens from humans. We conducted a literature review on occurrences of pathogen transmission from humans to great apes to highlight this often underappreciated issue. In total, we found 33 individual occurrences of probable or confirmed pathogen transmission from humans to great apes: 23 involved both pathogen and disease transmission, 7 pathogen transmission only, 2 positive antibody titers to zoonotic pathogens, and 1 pathogen transmission with probable disease. Great ape populations were categorized into captive, semi-free-living, and free-living conditions. The majority of occurrences involved chimpanzees (Pan troglodytes) (n = 23) or mountain gorillas (Gorilla beringei beringei) (n = 8). These findings have implications for conservation efforts and management of endangered great ape populations. Future efforts should focus on monitoring and addressing zoonotic pathogen and disease transmission between humans, great ape species, and other taxa to ensure the health of humans, wild and domestic animals, and the ecosystems we share.

Emergence and Evolution of Hominidae-Specific Coding and Noncoding Genomic Sequences.

Family Hominidae, which includes humans and great apes, is recognized for unique complex social behavior and intellectual abilities. Despite the increasing genome data, however, the genomic origin of its phenotypic uniqueness has remained elusive. Clade-specific genes and highly conserved noncoding sequences (HCNSs) are among the high-potential evolutionary candidates involved in driving clade-specific characters and phenotypes. On this premise, we analyzed whole genome sequences along with gene orthology data retrieved from major DNA databases to find Hominidae-specific (HS) genes and HCNSs. We discovered that Down syndrome critical region 4 (DSCR4) is the only experimentally verified gene uniquely present in Hominidae. DSCR4 has no structural homology to any known protein and was inferred to have emerged in several steps through LTR/ERV1, LTR/ERVL retrotransposition, and transversion. Using the genomic distance as neutral evolution threshold, we identified 1,658 HS HCNSs. Polymorphism coverage and derived allele frequency analysis of HS HCNSs showed that these HCNSs are under purifying selection, indicating that they may harbor important functions. They are overrepresented in promoters/untranslated regions, in close proximity of genes involved in sensory perception of sound and developmental process, and also showed a significantly lower nucleosome occupancy probability. Interestingly, many ancestral sequences of the HS HCNSs showed very high evolutionary rates. This suggests that new functions emerged through some kind of positive selection, and then purifying selection started to operate to keep these functions.

The hominins: a very conservative tribe? Last common ancestors, plasticity and ecomorphology in Hominidae. Or, What's in a name?

In the early 20th century the dominant paradigm for the ecological context of the origins of human bipedalism was arboreal suspension. In the 1960s, however, with recognition of the close genetic relationship of humans, chimpanzees and bonobos, and with the first field studies of mountain gorillas and common chimpanzees, it was assumed that locomotion similar to that of common chimpanzees and mountain gorillas, which appeared to be dominated by terrestrial knuckle-walking, must have given rise to human bipedality. This paradigm has been popular, if not universally dominant, until very recently. However, evidence that neither the knuckle-walking or vertical climbing of these apes is mechanically similar to human bipedalism, as well as the hand-assisted bipedality and orthograde clambering of orang-utans, has cast doubt on this paradigm. It now appears that the dominance of terrestrial knuckle-walking in mountain gorillas is an artefact seen only in the extremes of their range, and that both mountain and lowland gorillas have a generalized orthogrady similar to that seen in orang-utans. These data, together with evidence for continued arboreal competence in humans, mesh well with an increasing weight of fossil evidence suggesting that a mix of orang-utan and gorilla-like arboreal locomotion and upright terrestrial bipedalism characterized most australopiths. The late split date of the panins, corresponding to dates for separation of Homo and Australopithecus, leads to the speculation that competition with chimpanzees, as appears to exist today with gorillas, may have driven ecological changes in hominins and perhaps cladogenesis. However, selection for ecological plasticity and morphological conservatism is a core characteristic of Hominidae as a whole, including Hominini.

In vitro strain in human metacarpal bones during striking: testing the pugilism hypothesis of hominin hand evolution.

The hands of hominins (i.e. bipedal apes) are distinguished by skeletal proportions that are known to enhance manual dexterity but also allow the formation of a clenched fist. Because male-male physical competition is important in the mating systems of most species of great apes, including humans, we tested the hypothesis that a clenched fist protects the metacarpal bones from injury by reducing the level of strain during striking. We used cadaver arms to measure in vitro strain in metacarpals during forward strikes with buttressed and unbuttressed fist postures and during side slaps with an open palm. If the protective buttressing hypothesis is correct, the clenched fist posture should substantially reduce strain in the metacarpal bones during striking and therefore reduce the risk of fracture. Recorded strains were significantly higher in strikes in which the hand was secured in unbuttressed and slapping postures than in the fully buttressed posture. Our results suggest that humans can safely strike with 55% more force with a fully buttressed fist than with an unbuttressed fist and with twofold more force with a buttressed fist than with an open-hand slap. Thus, the evolutionary significance of the proportions of the hominin hand may be that these are the proportions that improved manual dexterity while at the same time making it possible for the hand to be used as a club during fighting.

The vertebral remains of the late Miocene great ape Hispanopithecus laietanus from Can Llobateres 2 (Vallès-Penedès Basin, NE Iberian Peninsula).

Here we describe the vertebral fragments from the partial skeleton IPS18800 of the fossil great ape Hispanopithecus laietanus (Hominidae: Dryopithecinae) from the late Miocene (9.6 Ma) of Can Llobateres 2 (Vallès-Penedès Basin, Catalonia, Spain). The eight specimens (IPS18800.5-IPS18800.12) include a fragment of thoracic vertebral body, three partial bodies and four neural arch fragments of lumbar vertebrae. Despite the retention of primitive features (moderately long lumbar vertebral bodies with slightly concave ventrolateral sides), these specimens display a suite of derived, modern hominoid-like features: thoracic vertebrae with dorsally-situated costal foveae; lumbar vertebrae with non-ventrally-oriented transverse processes originating from a robust pedicle, caudally-long laminae with caudally-oriented spinous process, elliptical end-plates, and moderately stout bodies reduced in length and with no ventral keel. These features, functionally related to orthograde behaviors, are indicative of a broad and shallow thorax with a moderately short and stiff lumbar region in Hispanopithecus. Despite its large body mass (ca. 39-40 kg), its vertebral morphology is more comparable to that of hylobatids and Ateles than to extant great apes. This is confirmed by our morphometric analyses, also indicating that Hispanopithecus most closely resembles Pierolapithecus and Morotopithecus among Miocene apes, whereas Proconsul and Nacholapithecus resemble pronograde monkeys. Only in a few features (craniocaudally short and transversely wide pedicles, transverse processes situated on the pedicle, and slight ventral wedging), Hispanopithecus is more derived towards the extant great ape condition than other Miocene apes. Overall, the vertebral morphology of Hispanopithecus supports previous inferences of an orthograde body plan with suspensory and climbing adaptations. However, given similarities with Ateles and the retention of a longer and more flexible spine than in extant great apes, the Hispanopithecus morphology is also consistent with some degree of above-branch quadrupedalism, as previously inferred from other anatomical regions.