scholarly journals Correlated and geographically predictable Neanderthal and Denisovan legacies are difficult to reconcile with a simple model based on inter-breeding

2021 ◽  
Vol 8 (6) ◽  
pp. 201229
Author(s):  
William Amos
Keyword(s):  
North Africa ◽  
Common Ancestor ◽  
Test Group ◽  
Great Apes ◽  
Strongly Correlated ◽  
Genome Diversity ◽  
Large Dataset ◽  
Neutral Drift ◽  
Out Of Africa ◽  
Project Data

Although the presence of archaic hominin legacies in humans is taken for granted, little attention has been given as to how the data fit with how humans colonized the world. Here, I show that Neanderthal and Denisovan legacies are strongly correlated and that inferred legacy size, like heterozygosity, exhibits a strong correlation with distance from Africa. Simulations confirm that, once created, legacy size is extremely stable: it may reduce through admixture with lower legacy populations but cannot increase significantly through neutral drift. Consequently, populations carrying the highest legacies are likely to be those whose ancestors inter-bred most with archaics. However, the populations with the highest legacies are globally scattered and are unified, not by having origins within the known Neanderthal range, but instead by living in locations that lie furthest from Africa. Furthermore, the Simons Genome Diversity Project data reveal two distinct correlations between Neanderthal and Denisovan legacies, one that starts in North Africa and increases west to east across Eurasia and into some parts of Oceania, and a second, much steeper trend that starts in Africa, peaking with the San and Ju/’hoansi and which, if extrapolated, predicts the large inferred legacies of both archaics found in Oceania/Australia. Similar ‘double’ trends are observed for the introgression statistic f 4 in a second large dataset published by Qin and Stoneking (Qin & Stoneking 2015 Mol. Biol. Evol. 32 , 2665–2674 ( doi:10.1093/molbev/msv141 )). These trends appear at odds with simple models of how introgression occurred though more complicated patterns of introgression could potentially generate better fits. Moreover, substituting archaic genomes with those of great apes yields similar but biologically impossible signals of introgression, suggesting that the signals these metrics capture arise within humans and are largely independent of the test group. Interestingly, the data do appear to fit a speculative model in which the loss of diversity that occurred when humans moved further from Africa created a gradient in heterozygosity that in turn progressively reduced mutation rate such that populations furthest from Africa have diverged less from our common ancestor and hence from the archaics. In this light, the two distinct trends could be interpreted in terms of two ‘out of Africa’ events, an early one ending in Oceania and Australia and a later one that colonized Eurasia and the Americas.

Only in Africa

2021 ◽  
Author(s):  
Norman Owen-Smith
Keyword(s):  
Plate Tectonics ◽  
Common Ancestor ◽  
Great Apes ◽  
Modern Humans ◽  
Evolutionary Transitions ◽  
Distinctive Features ◽  
Out Of Africa ◽  
Physical Features

That humans originated from Africa is well-known. However, this is widely regarded as a chance outcome, dependant simply on where our common ancestor shared the land with where the great apes lived. This volume builds on from the 'Out of Africa' theory, and takes the view that it is only in Africa that the evolutionary transitions from a forest-inhabiting frugivore to savanna-dwelling meat-eater could have occurred. This book argues that the ecological circumstances that shaped these transitions are exclusive to Africa. It describes distinctive features of the ecology of Africa, with emphasis on savanna grasslands, and relates them to the evolutionary transitions linking early ape-men to modern humans. It shows how physical features of the continent, especially those derived from plate tectonics, set the foundations. This volume adequately conveys that we are here because of the distinctive features of the ecology of Africa.

scholarly journals Experimental evidence for yawn contagion in orangutans (Pongo pygmaeus)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Evy van Berlo ◽  
Alejandra P. Díaz-Loyo ◽  
Oscar E. Juárez-Mora ◽  
Mariska E. Kret ◽  
Jorg J. M. Massen
Keyword(s):  
Experimental Evidence ◽  
Common Ancestor ◽  
Great Apes ◽  
Pongo Pygmaeus ◽  
Last Common Ancestor ◽  
Contagious Yawning ◽  
Proximate Mechanism ◽  
Social Species ◽  
Ultimate Causation

AbstractYawning 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.

scholarly journals Fluctuating Asymmetry and Sexual Dimorphism in Human Facial Morphology: A Multi-Variate Study

Symmetry ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 304
Author(s):  
Omid Ekrami ◽  
Peter Claes ◽  
Ellen Van Assche ◽  
Mark D. Shriver ◽  
Seth M. Weinberg ◽  
...  
Keyword(s):  
Fluctuating Asymmetry ◽  
Life History Traits ◽  
Principal Component ◽  
Underlying Mechanism ◽  
High Density ◽  
Direct Result ◽  
Facial Morphology ◽  
Strongly Correlated ◽  
Large Dataset ◽  
Genetic Quality

(1) Background: Fluctuating asymmetry is often used as an indicator of developmental instability, and is proposed as a signal of genetic quality. The display of prominent masculine phenotypic features, which are a direct result of high androgen levels, is also believed to be a sign of genetic quality, as these hormones may act as immunosuppressants. Fluctuating asymmetry and masculinity are therefore expected to covary. However, there is lack of strong evidence in the literature regarding this hypothesis. (2) Materials and methods: In this study, we examined a large dataset of high-density 3D facial scans of 1260 adults (630 males and 630 females). We mapped a high-density 3D facial mask onto the facial scans in order to obtain a high number of quasi-landmarks on the faces. Multi-dimensional measures of fluctuating asymmetry were extracted from the landmarks using Principal Component Analysis, and masculinity/femininity scores were obtained for each face using Partial Least Squares. The possible correlation between these two qualities was then examined using Pearson’s coefficient and Canonical Correlation Analysis. (3) Results: We found no correlation between fluctuating asymmetry and masculinity in men. However, a weak but significant correlation was found between average fluctuating asymmetry and masculinity in women, in which feminine faces had higher levels of fluctuating asymmetry on average. This correlation could possibly point to genetic quality as an underlying mechanism for both asymmetry and masculinity; however, it might also be driven by other fitness or life history traits, such as fertility. (4) Conclusions: Our results question the idea that fluctuating asymmetry and masculinity should be (more strongly) correlated in men, which is in line with the recent literature. Future studies should possibly focus more on the evolutionary relevance of the observed correlation in women.

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

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Naoki Morimoto ◽  
Masato Nakatsukasa ◽  
Marcia S. Ponce de León ◽  
Christoph P. E. Zollikofer
Keyword(s):  
Common Ancestor ◽  
Great Apes ◽  
Last Common Ancestor

scholarly journals Using Deep Learning with Large Dataset of Microscope Images to Develop an Automated Embryo Grading System

2019 ◽  
Vol 01 (01) ◽  
pp. 51-56 ◽  
Author(s):  
Tsung-Jui Chen ◽  
Wei-Lin Zheng ◽  
Chun-Hsin Liu ◽  
Ian Huang ◽  
Hsing-Hua Lai ◽  
...  
Keyword(s):  
Deep Learning ◽  
Visual Analysis ◽  
Predictive Accuracy ◽  
Test Group ◽  
Training Group ◽  
Grading System ◽  
Embryo Viability ◽  
Blastocyst Development ◽  
Large Dataset ◽  
Embryo Grading

The assessment of embryo viability for in vitro fertilization (IVF) is mainly based on subjective visual analysis, with the limitation of intra- and inter-observer variation and a time-consuming task. In this study, we used deep learning with large dataset of microscopic embryo images to develop an automated grading system for embryo assessment. This study included a total of 171,239 images from 16,201 embryos of 4,146 IVF cycles at Stork Fertility Center (https://www.e-stork.com.tw) from March 6, 2014 to April 13, 2018. The images were captured by inverted microscope (Zeiss Axio Observer Z1) at 112 to 116 hours (Day 5) or 136 to 140 hours (Day 6) after fertilization. Using a pre-trained network trained on the ImageNet dataset as convolution base, we applied Convolutional Neural Network (CNN) on embryo images, using ResNet50 architecture to fine-tune ImageNet parameters. The predicted grading results was compared with the grading results from trained embryologists to evaluate the model performance. The images were labeled by trained embryologists, based on Gardner’s grading system: blastocyst development ranking from 3–6, ICM quality as A, B, or C; and TE quality as a, b, or c. After pre-processing, the images were divided into training, validation, and test groups, in which 60% were allocated to the training group, 20% to the validation group, and 20% to the test group. The ResNet50 algorithm was trained on the 60% images allocated to the training group, and the algorithm’s performance was evaluated using the 20% images allocated to the test group. The results showed an average predictive accuracy of 75.36% for the all three grading categories: 96.24% for blastocyst development, 91.07% for ICM quality, and 84.42% for TE quality. To the best of our knowledge, this is the first study of an automatic embryo grading system using large dataset from Asian population. Combing the promising results obtained in this study with time-lapse microscope system integrated with IVF Electronic Medical Record platform, a fully automated and non-invasive pipeline for embryo assessment will be achieved.

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

2019 ◽  
Author(s):  
Keaghan J Yaxley ◽  
Robert A Foley
Keyword(s):  
Dna Sequences ◽  
Phenotypic Variation ◽  
Common Ancestor ◽  
Phylogenetic Signal ◽  
Great Apes ◽  
Last Common Ancestor ◽  
Ancestral State ◽  
Great Ape ◽  
Subspecies Level ◽  
African Great Apes

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.

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

2018 ◽  
Vol 19 (1-2) ◽  
pp. 370-387 ◽  
Author(s):  
Michael A. Arbib ◽  
Francisco Aboitiz ◽  
Judith M. Burkart ◽  
Michael Corballis ◽  
Gino Coudé ◽  
...  
Keyword(s):  
Comparative Study ◽  
Cultural Evolution ◽  
Common Ancestor ◽  
Great Apes ◽  
Last Common Ancestor ◽  
Road Map ◽  
The Rich ◽  
The Comparative Study ◽  
Brain Behavior ◽  
The Brain

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.

Discovering Human Nature Through Cross-Species Analysis

2018 ◽  
Author(s):  
Jonathan H. Turner
Keyword(s):  
Human Nature ◽  
Common Ancestor ◽  
Cladistic Analysis ◽  
Great Apes ◽  
The Body ◽  
Last Common Ancestor ◽  
Species Analysis ◽  
Organizational Patterns ◽  
Genetic Closeness ◽  
Source Of Information

Cladistic analysis is employed on behavioral and organizational patterns among present-day great apes that, because of their genetic closeness to humans, can be used as a surrogate for making inferences about the behavior and organizational propensities of the last common ancestor to great apes, hominins, and humans. A series of preadaptations among great apes for language, emotionality, mother–infant bonding, life history characteristics, propensities for play, and nonharem/promiscuous mating represents one source of information on the nature of the last common ancestor. Moreover, a set of behavioral propensities among all great apes adds to the body of information that can be used to make inferences about the nature of the last common ancestors, hominins, and humans. Thus, it is now possible to make inferences about the biological nature of human behavior and organizational tendencies that are less speculative than earlier analyses of human nature.

scholarly journals Genetic Differences Between Humans and Great Apes –Implications for the Evolution of Humans

2004 ◽  
Vol 213 ◽  
pp. 343-348
Author(s):  
Ajit Varki
Keyword(s):  
Common Ancestor ◽  
Great Apes ◽  
Human Condition ◽  
Microbial Pathogens ◽  
Mammalian Brain ◽  
Gene Products ◽  
Social Origin ◽  
Surface Molecules ◽  
Oncofetal Antigens ◽  
Human Brain Development

At the level of individual protein sequences, humans are 97–100% identical to the great apes, our closest evolutionary relatives. The evolution of humans (and of human intelligence) from a common ancestor with the chimpanzee and bonobo involved many steps, influenced by interactions amongst factors of genetic, developmental, ecological, microbial, climatic, behavioral, cultural and social origin. The genetic factors can be approached by direct comparisons of human and great ape genomes, genes and gene products, and by elucidating biochemical and biological consequences of any differences found. We have discovered multiple genetic and biochemical differences between humans and great apes, particularly with respect to a family of cell surface molecules called sialic acids, as well as in the metabolism of thyroid hormones. The hormone differences have potential consequences for human brain development. The differences in sialic acid biology have multiple implications for the human condition, ranging from susceptibility or resistance to microbial pathogens, effects on endogenous receptors in the immune system, and potential effects on placental signaling, expression of oncofetal antigens in cancers, consequences of dietary intake of animal foods, and development of the mammalian brain.

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