Last Common Ancestor Of Humans Research Articles

Ulnar morphology in Sahelanthropus tchadensis, what it tells us on the locomotor repertoire of the last common ancestor of humans and

Ulnar morphology in Sahelanthropus tchadensis, what it tells us on the locomotor repertoire of the last common ancestor of humans and

Evolution of vertebral numbers in primates, with a focus on hominoids and the last common ancestor of hominins and panins

The primate vertebral column has been extensively studied, with a particular focus on hominoid primates and the last common ancestor of humans and chimpanzees. The number of vertebrae in hominoids—up to and including the last common ancestor of humans and chimpanzees—is subject to considerable debate. However, few formal ancestral state reconstructions exist, and none include a broad sample of primates or account for the correlated evolution of the vertebral column. Here, we conduct an ancestral state reconstruction using a model of evolution that accounts for both homeotic (changes of one type of vertebra to another) and meristic (addition or loss of a vertebra) changes. Our results suggest that ancestral primates were characterized by 29 precaudal vertebrae, with the most common formula being seven cervical, 13 thoracic, six lumbar, and three sacral vertebrae. Extant hominoids evolved tail loss and a reduced lumbar column via sacralization (homeotic transition at the last lumbar vertebra). Our results also indicate that the ancestral hylobatid had seven cervical, 13 thoracic, five lumbar, and four sacral vertebrae, and the ancestral hominid had seven cervical, 13 thoracic, four lumbar, and five sacral vertebrae. The last common ancestor of humans and chimpanzees likely either retained this ancestral hominid formula or was characterized by an additional sacral vertebra, possibly acquired through a homeotic shift at the sacrococcygeal border. Our results support the ‘short-back’ model of hominin vertebral evolution, which postulates that hominins evolved from an ancestor with an African ape–like numerical composition of the vertebral column.

Homeotic change in segment identity derives the human vertebral formula from a chimpanzee‐like one

One of the most contentious issues in paleoanthropology is the nature of the last common ancestor of humans and our closest living relatives, chimpanzees and bonobos (panins). The numerical composition of the vertebral column has featured prominently, with multiple models predicting distinct patterns of evolution and contexts from which bipedalism evolved. Here, we study total numbers of vertebrae from a large sample of hominoids to quantify variation in and patterns of regional and total numbers of vertebrae in hominoids. We compile and study a large sample (N=893) of hominoid vertebral formulae (numbers of cervical, thoracic, lumbar, sacral, caudal segments in each specimen) and analyze full vertebral formulae, total numbers of vertebrae, and super-regional numbers of vertebrae: presacral (cervical, thoracic, lumbar) vertebrae and sacrococcygeal vertebrae. We quantify within- and between-taxon variation using heterogeneity and similarity measures derived from population genetics. We find that humans are most similar to African apes in total and super-regional numbers of vertebrae. Additionally, our analyses demonstrate that selection for bipedalism reduced variation in numbers of vertebrae relative to other hominoids. The only proposed ancestral vertebral configuration for the last common ancestor of hominins and panins that is consistent with our results is the modal formula demonstrated by chimpanzees and bonobos (7 cervical-13 thoracic-4 lumbar-6 sacral-3 coccygeal). Hox gene expression boundaries suggest that a rostral shift in Hox10/Hox11-mediated complexes could produce the human modal formula from the proposal ancestral and panin modal formula.

Experimental evidence for yawn contagion in orangutans (Pongo pygmaeus)

Yawning is highly contagious, yet both its proximate mechanism(s) and its ultimate causation remain poorly understood. Scholars have suggested a link between contagious yawning (CY) and sociality due to its appearance in mostly social species. Nevertheless, as findings are inconsistent, CY’s function and evolution remains heavily debated. One way to understand the evolution of CY is by studying it in hominids. Although CY has been found in chimpanzees and bonobos, but is absent in gorillas, data on orangutans are missing despite them being the least social hominid. Orangutans are thus interesting for understanding CY’s phylogeny. Here, we experimentally tested whether orangutans yawn contagiously in response to videos of conspecifics yawning. Furthermore, we investigated whether CY was affected by familiarity with the yawning individual (i.e. a familiar or unfamiliar conspecific and a 3D orangutan avatar). In 700 trials across 8 individuals, we found that orangutans are more likely to yawn in response to yawn videos compared to control videos of conspecifics, but not to yawn videos of the avatar. Interestingly, CY occurred regardless of whether a conspecific was familiar or unfamiliar. We conclude that CY was likely already present in the last common ancestor of humans and great apes, though more converging evidence is needed.

Spontaneous (minimal) ritual in non-human great apes?

The potential for rituals in non-human great apes (apes) is an understudied topic. We derive a minimal definition of ritual and then examine the currently available evidence for it in untrained and non-enculturated apes. First, we examine whether such apes show evidence for the two main components of our minimal definition of ritual: symbolism and copying. Second, we examine if there are actual cases already identifiable today that may fit all aspects of our minimal definition of ritual-or whether there are at least cases that fit some aspects (proto-ritual). We find that apes are not likely to spontaneously practise minimal ritual, but we claim that the highest expected likelihood of occurrence is in the results-copying domain. Yet, we did not find actual cases of minimal ritual in apes-including those involving environmental results. We did, however, find some cases that may match at least part of our minimal ritual definition-which we termed proto-ritual. At least two out of three potential cases of such proto-rituals that we identified (rain dance, object-in-ear and surplus nest-making procedures) do revolve around results. Overall, apes do not show much, or very clear, evidence for even minimal ritual, but may sometimes show proto-ritual. However, dedicated ape ritual studies are currently lacking, and future work may identify ape ritual (or clearer cases of proto-ritual). We discuss the implications of our preliminary finding for inferences of ritual in the last common ancestor of humans and apes. This article is part of the theme issue 'Ritual renaissance: new insights into the most human of behaviours'.

Human Carpal Evolution and its Implications for Hominin Locomotor Ancestry

The ancestral locomotor repertoire from which hominin bipedalism emerged remains a subject of frequent debate, with multiple competing hypotheses maintaining support among active researchers. This study contributes to this ongoing debate by reconstructing the morphological and locomotor evolution of hominoids based on patterns of morphometric variation in the capitate, hamate, lunate, and triquetrum among extant and fossil anthropoids, including humans and fossil hominins. Aspects of carpal morphology found to consistently covary with locomotor behavior are used to reconstruct adaptive transitions within the anthropoid clade associated with locomotor behavior. The prevalence of different locomotor behaviors at the origin of nested clades within Hominoidea, including the one we share with Pan, are also estimated.While there is some inconsistency of morphological covariation with function and phylogeny among carpal elements, results are consistent in supporting frequent parallelism during hominoid locomotor evolution. This support is strongest as it applies to suspensory behaviors, with the last common ancestors of both apes and great apes predicted to have remained quite generalized relative to the clades’ extant representatives. The last common ancestor of humans and chimpanzees/bonobos is also estimated to have lacked adaptations in association with knuckle‐walking, providing further support for the hominin clade having descended from a relatively generalized ancestral morphotype that is not well modeled by any of the surviving hominoid lineages.

First evidence of a new simian adenovirus clustering with Human mastadenovirusF viruses

BackgroundAdenoviruses play an important role as human pathogens, though most infections are believed to be asymptomatic. The over 100 human adenovirus types are classified into seven species (A-G), some of which include simian adenoviruses. Recent findings have highlighted that simian adenoviruses have a zoonotic potential and that some human adenoviruses are likely the result of relatively recent spillover events.MethodsIn order to evaluate the risks associated with primates hunted and sold as bushmeat, multiple samples from 24 freshly killed monkeys were collected in the Republic of the Congo and tested for adenovirus DNA by PCRs targeting the conserved DNA polymerase and hexon genes.ResultsThe DNA of a novel simian adenovirus was detected in a moustached monkey (Cercopithecus cephus) by the DNA polymerase PCR, but not by the hexon PCR. The 275 nucleotide amplicon was most closely related to members of the Human mastadenovirusF species (93% HAdV-40 and 89% HAdV-41 amino acid identity), rather than to other known simian adenoviruses.ConclusionsThe phylogenetic clustering with Human mastadenovirusF sequences suggests a common ancestor, more recent than the last common ancestor of humans and moustached monkeys. The findings increase concerns about the zoonotic potential of simian adenoviruses and highlight the need for more research and surveillance on the issue.

DALI and the persistence of protein shape.

DALI is a popular resource for comparing protein structures. The software is based on distance-matrix alignment. The associated web server provides tools to navigate, integrate and organize some data pushed out by genomics and structural genomics. The server has been running continuously for the past 25 years. Structural biologists routinely use DALI to compare a new structure against previously known protein structures. If significant similarities are discovered, it may indicate a distant homology, that is, that the structures are of shared origin. This may be significant in determining the molecular mechanisms, as these may remain very similar from a distant predecessor to the present day, for example, from the last common ancestor of humans and bacteria. Meta-analysis of independent reference-based evaluations of alignment accuracy and fold discrimination shows DALI at top rank in six out of 12 studies. The web server and standalone software are available from http://ekhidna2.biocenter.helsinki.fi/dali.

Reconstructing the ancestral phenotypes of great apes and humans (Homininae) using subspecies-level phylogenies

Abstract Owing to their close affinity, the African great apes are of interest in the study of human evolution. Although numerous researchers have described the ancestors we share with these species with reference to extant great apes, few have done so with phylogenetic comparative methods. One obstacle to the application of these techniques is the within-species phenotypic variation found in this group. Here, we leverage this variation, modelling common ancestors using ancestral state reconstructions (ASRs) with reference to subspecies-level trait data. A subspecies-level phylogeny of the African great apes and humans was estimated from full-genome mitochondrial DNA sequences and used to implement ASRs for 14 continuous traits known to vary between great ape subspecies. Although the inclusion of within-species phenotypic variation increased the phylogenetic signal for our traits and improved the performance of our ASRs, whether this was done through the inclusion of subspecies phylogeny or through the use of existing methods made little difference. Our ASRs corroborate previous findings that the last common ancestor of humans, chimpanzees and bonobos was a chimp-like animal, but also suggest that the last common ancestor of humans, chimpanzees, bonobos and gorillas was an animal unlike any extant African great ape.

Female Sex Development and Reproductive Duct Formation Depend on Wnt4a in Zebrafish.

In laboratory strains of zebrafish, sex determination occurs in the absence of a typical sex chromosome and it is not known what regulates the proportion of animals that develop as males or females. Many sex determination and gonad differentiation genes that act downstream of a sex chromosome are well conserved among vertebrates, but studies that test their contribution to this process have mostly been limited to mammalian models. In mammals, WNT4 is a signaling ligand that is essential for ovary and Müllerian duct development, where it antagonizes the male-promoting FGF9 signal. Wnt4 is well conserved across all vertebrates, but it is not known if Wnt4 plays a role in sex determination and/or the differentiation of sex organs in nonmammalian vertebrates. This question is especially interesting in teleosts, such as zebrafish, because they lack an Fgf9 ortholog. Here we show that wnt4a is the ortholog of mammalian Wnt4, and that wnt4b was present in the last common ancestor of humans and zebrafish, but was lost in mammals. We show that wnt4a loss-of-function mutants develop predominantly as males and conclude that wnt4a activity promotes female sex determination and/or differentiation in zebrafish. Additionally, both male and female wnt4a mutants are sterile due to defects in reproductive duct development. Together these results strongly argue that Wnt4a is a conserved regulator of female sex determination and reproductive duct development in mammalian and nonmammalian vertebrates.

The comparative neuroprimatology 2018 (CNP-2018) road map for research on How the Brain Got Language

Abstract We present a new road map for research on “How the Brain Got Language” that adopts an EvoDevoSocio perspective and highlights comparative neuroprimatology – the comparative study of brain, behavior and communication in extant monkeys and great apes – as providing a key grounding for hypotheses on the last common ancestor of humans and monkeys (LCA-m) and chimpanzees (LCA-c) and the processes which guided the evolution LCA-m → LCA-c → protohumans → H. sapiens. Such research constrains and is constrained by analysis of the subsequent, primarily cultural, evolution of H. sapiens which yielded cultures involving the rich use of language.

Femoral ontogeny in humans and great apes and its implications for their last common ancestor

Inferring the morphology of the last common ancestor of humans, chimpanzees and gorillas is a matter of ongoing debate. Recent findings and reassessment of fossil hominins leads to the hypothesis that the last common ancestor was not extant African ape-like. However, an African great-ape-like ancestor with knuckle walking features still remains plausible and the most parsimonious scenario. Here we address this question via an evolutionary developmental approach, comparing taxon-specific patterns of shape change of the femoral diaphysis from birth to adulthood in great apes, humans, and macaques. While chimpanzees and gorillas exhibit similar locomotor behaviors, our data provide evidence for distinct ontogenetic trajectories, indicating independent evolutionary histories of femoral ontogeny. Our data further indicate that anthropoid primates share a basic pattern of femoral diaphyseal ontogeny that reflects shared developmental constraints. Humans escaped from these constraints via differential elongation of femur.

Resurrecting KIR2DP1: A Key Intermediate in the Evolution of Human Inhibitory NK Cell Receptors That Recognize HLA-C.

KIR2DP1 is an inactive member of the human lineage III KIR family, which includes all HLA-C-specific receptor genes. The lethal, and only, defect in KIR2DP1 is a nucleotide deletion in codon 88. Fixed in modern humans, the deletion is also in archaic human genomes. KIR2DP1 is polymorphic, with dimorphism at specificity-determining position 44. By repairing the deletion, we resurrected 11 alleles of KIR2DP1F , the functional antecedent of KIR2DP1 We demonstrate how K44-KIR2DP1F with lysine 44 recognized C1+HLA-C, whereas T44-KIR2DP1F recognized C2+HLA-C. Dimorphisms at 12 other KIR2DP1F residues modulate receptor avidity or signaling. KIR2DP1 and KIR2DL1 are neighbors in the centromeric KIR region and are in tight linkage disequilibrium. Like KIR2DL1, KIR2DP1 contributed to CenA and CenB KIR haplotype differences. Encoded on CenA, C1-specific K44-KIR2DP1F were stronger receptors than the attenuated C2-specific T44-KIR2DP1F encoded on CenB The last common ancestor of humans and chimpanzees had diverse lineage III KIR that passed on to chimpanzees but not to humans. Early humans inherited activating KIR2DS4 and an inhibitory lineage III KIR, likely encoding a C1-specific receptor. The latter spawned the modern family of HLA-C receptors. KIR2DP1F has properties consistent with KIR2DP1F having been the founder gene. The first KIR2DP1F alleles encoded K44-C1 receptors; subsequently KIR2DP1F alleles encoding T44-C2 receptors evolved. The emergence of dedicated KIR2DL2/3 and KIR2DL1 genes encoding C1 and C2 receptors, respectively, could have led to obsolescence of KIR2DP1F Alternatively, pathogen subversion caused its demise. Preservation of KIR2DP1F functional polymorphism was a side effect of fixation of the deletion in KIR2DP1F by micro gene conversion.

Fossil hominin shoulders support an African ape-like last common ancestor of humans and chimpanzees

Reconstructing the behavioral shifts that drove hominin evolution requires knowledge of the timing, magnitude, and direction of anatomical changes over the past ∼6-7 million years. These reconstructions depend on assumptions regarding the morphotype of the Homo-Pan last common ancestor (LCA). However, there is little consensus for the LCA, with proposed models ranging from African ape to orangutan or generalized Miocene ape-like. The ancestral state of the shoulder is of particular interest because it is functionally associated with important behavioral shifts in hominins, such as reduced arboreality, high-speed throwing, and tool use. However, previous morphometric analyses of both living and fossil taxa have yielded contradictory results. Here, we generated a 3D morphospace of ape and human scapular shape to plot evolutionary trajectories, predict ancestral morphologies, and directly test alternative evolutionary hypotheses using the hominin fossil evidence. We show that the most parsimonious model for the evolution of hominin shoulder shape starts with an African ape-like ancestral state. We propose that the shoulder evolved gradually along a single morphocline, achieving modern human-like configuration and function within the genus Homo. These data are consistent with a slow, progressive loss of arboreality and increased tool use throughout human evolution.

The limiting distribution of the effective population size of the ancestor of humans and chimpanzees

The effective population size is a fundamental parameter for the understanding of microevolutionary process. Indeed, the consideration of population-level phenomena within phylogenies provides insight into the influence of the past evolutionary demography on the genetic diversity of living species. Although the effective population size of the last common ancestor of humans and chimpanzees has been extensively investigated by molecular evolutionists, variance in the estimates of this parameter among studies is large. However, with the availability of genome sequences, the estimation of evolutionary parameters may be conducted with minimum stochastic error, and the limiting distribution of the estimates may be obtained. This statistical property was utilized in the present study and coupled with analytical derivations from the coalescent theory to examine the limiting distribution of the ancestral effective population size of Homo–Pan. The mean ancestral effective population size of Homo–Pan was inferred at approximately 47,500, and the results showed that the uncertainty of the estimates was large, even under the limiting distribution. Further reductions of the estimates are feasible only if additional calibration information from the fossil record is provided and if a probabilistic model of ancestral generation time is envisioned.

On the tool use behavior of the bonobo‐chimpanzee last common ancestor, and the origins of hominine stone tool use

The last common ancestor (LCA) shared by chimpanzees (Pan troglodytes) and bonobos (P. paniscus) was an Early Pleistocene African ape, which, based on the behavior of modern chimpanzees, may be assumed to be a tool-using animal. However, the character of tool use in the Pan lineage prior to the 20th century is largely unknown. Here, I use available data on wild bonobo tool use and emerging molecular estimates of demography during Pan evolution to hypothesise the plausible tool use behavior of the bonobo-chimpanzee LCA (or "Pancestor") at the start of the Pleistocene, over 2 million years ago. This method indicates that the common ancestor of living Pan apes likely used plant tools for probing, sponging, and display, but it did not use stone tools. Instead, stone tool use appears to have been independently invented by Western African chimpanzees (P. t. verus) during the Middle Pleistocene in the region of modern Liberia-Ivory Coast-Guinea, possibly as recently as 200,000-150,000 years ago. If this is the case, then the LCA of humans and chimpanzees likely also did not use stone tools, and this trait probably first emerged among hominins in Pliocene East Africa. This review also suggests that the consistently higher population sizes of Central African chimpanzees (P. t. troglodytes) over the past million years may have contributed to the increased complexity of wild tool use seen in this sub-species today.

Chimpocentrism and reconstructions of human evolution (a timely reminder)

Chimpanzees, but very few other animals, figure prominently in (recent) attempts to reconstruct the evolution of uniquely human traits. In particular, the chimpanzee is used (i) to identify traits unique to humans, and thus in need of reconstruction; (ii) to initialize the reconstruction, by taking its state to reflect the state of the last common ancestor of humans and chimpanzees; (iii) as a baseline against which to test evolutionary hypotheses. Here I point out the flaws in this three-step procedure, and show how they can be overcome by taking advantage of much broader phylogenetic comparisons. More specifically, I explain how such comparisons yield more reliable estimations of ancestral states and how they help to resolve problems of underdetermination inherent to chimpocentric accounts. To illustrate my points, I use a recent chimpocentric argument by Kitcher.

The thumb of Miocene apes: New insights from Castell de Barberà (Catalonia, Spain)

Primate hands display a major selective compromise between locomotion and manipulation. The thumb may or may not participate in locomotion, but it plays a central role in most manipulative activities. Understanding whether or not the last common ancestor of humans and Pan displayed extant-ape-like hand proportions (i.e., relatively long fingers and a short thumb) can be clarified by the analysis of Miocene ape hand remains. Here we describe new pollical remains-a complete proximal phalanx and a partial distal phalanx-from the middle/late Miocene site of Castell de Barberà (ca., 11.2-10.5 Ma, Vallès-Penedès Basin), and provide morphometric and qualitative comparisons with other available Miocene specimens as well as extant catarrhines (including humans). Our results show that all available Miocene taxa (Proconsul, Nacholapithecus, Afropithecus, Sivapithecus, Hispanopithecus, Oreopithecus, and the hominoid from Castell de Barberà) share a similar phalangeal thumb morphology: the phalanges are relatively long, and the proximal phalanges have a high degree of curvature, marked insertions for the flexor muscles, a palmarly bent trochlea and a low basal height. All these features suggest that these Miocene apes used their thumb with an emphasis on flexion, most of them to powerfully assist the fingers during above-branch, grasping arboreal locomotion. Moreover, in terms of relative proximal phalangeal length, the thumb of Miocene taxa is intermediate between the long-thumbed humans and the short-thumbed extant apes. Together with previous evidence, this suggests that a moderate-length hand with relatively long thumb-involved in locomotion-is the original hand morphotype for the Hominidae.

Is Human Cell Therapy Research Caught in a Mousetrap?

About 65 million years ago, an asteroid the size of a city hit the Yucatan Peninsula, leading to the extinction of the dinosaurs. The impact fortuitously brought evolutionary opportunities for the last common ancestor of humans and mice to set out on the great radiation of mammals that today humans seem to be doing their best to deplete. Meanwhile, the mouse has been widely adopted as a model animal for understanding mammalian biology. Mice are at the forefront of animal research for many good reasons, not least their size, cost, life span, and availability in a myriad of well-defined strains.

A comparative approach shows differences in patterns of numt insertion during hominoid evolution.

Nuclear integrations of mitochondrial DNA (numts) are widespread among eukaryotes, although their prevalence differs greatly among taxa. Most knowledge of numt evolution comes from analyses of whole-genome sequences of single species or, more recently, from genomic comparisons across vast phylogenetic distances. Here we employ a comparative approach using human and chimpanzee genome sequence data to infer differences in the patterns and processes underlying numt integrations. We identified 66 numts that have integrated into the chimpanzee nuclear genome since the human-chimp divergence, which is significantly greater than the 37 numts observed in humans. By comparing these closely related species, we accurately reconstructed the preintegration target site sequence and deduced nucleotide changes associated with numt integration. From >100 species-specific numts, we quantified the frequency of small insertions, deletions, duplications, and instances of microhomology. Most human and chimpanzee numt integrations were accompanied by microhomology and short indels of the kind typically observed in the nonhomologous end-joining pathway of DNA double-strand break repair. Human-specific numts have integrated into regions with a significant deficit of transposable elements; however, the same was not seen in chimpanzees. From a separate data set, we also found evidence for an apparent increase in the rate of numt insertions in the last common ancestor of humans and the great apes using a polymerase chain reaction-based screen. Last, phylogenetic analyses indicate that mitochondrial-numt alignments must be at least 500 bp, and preferably >1 kb in length, to accurately reconstruct hominoid phylogeny and recover the correct point of numt insertion.