Sequence-Based Machine Learning Reveals 3D Genome Differences between Bonobos and Chimpanzees.

The 3D structure of the genome is an important mediator of gene expression. As phenotypic divergence is largely driven by gene regulatory variation, comparing genome 3D contacts across species can further understanding of the molecular basis of species differences. However, while experimental data on genome 3D contacts in humans are increasingly abundant, only a handful of 3D genome contact maps exist for other species.

Illuminating the function of the orphan transporter, SLC22A10, in humans and other primates.

SLC22A10 is an orphan transporter with unknown substrates and function. The goal of this study is to elucidate its substrate specificity and functional characteristics. In contrast to orthologs from great apes, human SLC22A10, tagged with green fluorescent protein, is not expressed on the plasma membrane.

Sequence-based machine learning reveals 3D genome differences between bonobos and chimpanzees.

Phenotypic divergence between closely related species, including bonobos and chimpanzees (genus ), is largely driven by variation in gene regulation. The 3D structure of the genome mediates gene expression; however, genome folding differences in are not well understood. Here, we apply machine learning to predict genome-wide 3D genome contact maps from DNA sequence for 56 bonobos and chimpanzees, encompassing all five extant lineages.

Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates.

SLC22A10 is classified as an orphan transporter with unknown substrates and function. Here we describe the discovery of the substrate specificity and functional characteristics of SLC22A10. The human SLC22A10 tagged with green fluorescent protein was found to be absent from the plasma membrane, in contrast to the SLC22A10 orthologs found in great apes.

Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates.

SLC22A10 is classified as an orphan transporter with unknown substrates and function. Here we describe the discovery of the substrate specificity and functional characteristics of SLC22A10. The human SLC22A10 tagged with green fluorescent protein was found to be absent from the plasma membrane, in contrast to the SLC22A10 orthologs found in great apes.

Resurrecting the alternative splicing landscape of archaic hominins using machine learning.

Alternative splicing contributes to adaptation and divergence in many species. However, it has not been possible to directly compare splicing between modern and archaic hominins. Here, we unmask the recent evolution of this previously unobservable regulatory mechanism by applying SpliceAI, a machine-learning algorithm that identifies splice-altering variants (SAVs), to high-coverage genomes from three Neanderthals and a Denisovan.

A comparison of faecal glucocorticoid metabolite concentration and gut microbiota diversity in bonobos ().

Sex, age, diet, stress and social environment have all been shown to influence the gut microbiota. In several mammals, including humans, increased stress is related to decreasing gut microbial diversity and may differentially impact specific taxa. Recent evidence from gorillas shows faecal glucocorticoid metabolite concentration (FGMC) did not significantly explain gut microbial diversity, but it was significantly associated with the abundance of the family Anaerolineaceae.

Estimating bonobo () and chimpanzee () evolutionary history from nucleotide site patterns.

Admixture appears increasingly ubiquitous in the evolutionary history of various taxa, including humans. Such gene flow likely also occurred among our closest living relatives: bonobos (Pan paniscus) and chimpanzees (Pan troglodytes). However, our understanding of their evolutionary history has been limited by studies that do not consider all Pan lineages or do not analyze all lineages simultaneously, resulting in conflicting demographic models.

Predicting Archaic Hominin Phenotypes from Genomic Data.

Ancient DNA provides a powerful window into the biology of extant and extinct species, including humans' closest relatives: Denisovans and Neanderthals. Here, we review what is known about archaic hominin phenotypes from genomic data and how those inferences have been made. We contend that understanding the influence of variants on lower-level molecular phenotypes-such as gene expression and protein function-is a promising approach to using ancient DNA to learn about archaic hominin traits.

A Test of Foraging Models Using Dietary Diversity Indices for the Lomako Forest Bonobos.

Optimal diet and functional response models are used to understand the evolution of primate foraging strategies. The predictions of these models can be tested by examining the geographic and seasonal variation in dietary diversity. Dietary diversity is a useful tool that allows dietary comparisons across differing sampling locations and time periods.

Age, sex, and inflammatory markers predict chronic conditions, cardiac disease, and mortality among captive western lowland gorillas (Gorilla gorilla gorilla).

In humans, inflammatory markers predict health risks. As great apes experience many similar conditions, measuring inflammation may provide valuable health information. We examined four serum inflammatory markers in zoo-housed gorillas (n = 48): albumin, CRP, IL-6, and TNF-α.

Sex differences in bonobo (Pan paniscus) terrestriality: implications for human evolution.

Recent finds in hominin fossil environments place the transition to terrestriality in a wooded or forested habitat. Therefore, forest-dwelling apes can aid in understanding this important evolutionary transition. Sex differences in ape locomotion have been previously attributed to sexual dimorphism or ecological niche differences between males and females.

Variation in Adult Male-Juvenile Affiliative Behavior in Japanese Macaques (Macaca fuscata).

Adult males of some primate species are known to positively interact with juveniles. In cases where paternal certainty is high, these behaviors have been largely attributed to the paternal investment hypothesis. Males have also been observed to interact with nonkin juveniles, which has often been explained in terms of mating effort.

Abundance, density, and social structure of African forest elephants (Loxodonta cyclotis) in a human-modified landscape in southwestern Gabon.

Population monitoring is critical to effective conservation, but forest living taxa can be difficult to directly observe. This has been true of African forest elephants (Loxodonta cyclotis), for which we have limited information regarding population size and social behavior despite their threatened conservation status. In this study, we estimated demographic parameters using genetic capture-recapture of forest elephants in the southern Industrial Corridor of the Gamba Complex of Protected Areas in southwestern Gabon, which is considered a global stronghold for forest elephants.

Social hair plucking is a grooming convention in a group of captive bonobos (Pan paniscus).

Hair plucking is observed in many captive primate species and is often characterized as an abnormal behavior. However, this behavior may be both self-directed and social and may have different etiologies. Early research in captive macaques (Macaca mulatta) described the aggressive nature of social hair plucking while more recent observations did not find an association with aggression or grooming, but the behavior was initiated most frequently by individuals with more secure dominance rank.

New Observations of Meat Eating and Sharing in Wild Bonobos (Pan paniscus) at Iyema, Lomako Forest Reserve, Democratic Republic of the Congo.

Bonobos (Pan paniscus) consume a variety of vertebrates, although direct observations remain relatively rare compared to chimpanzees (Pan troglodytes). We report the first direct observations of meat eating and sharing among bonobos at Iyema, Lomako Forest, Democratic Republic of Congo. We collected meat consumption data ad libitum from June to November 2017 over 176.

Infant handling in bonobos (Pan paniscus): Exploring functional hypotheses and the relationship to oxytocin.

Infant handling describes interactions between infants and non-maternal group members and is widespread across mammalian taxa. The expression of infant handling behaviors, defined as any affiliative or agonistic interaction between a group member and an infant, varies considerably among primate species. Several functional hypotheses may explain the adaptive value of infant handling including the Kin Selection hypothesis, which describes handling as a mechanism through which indirect fitness is increased and predicts a bias in handling behaviors directed toward related (genetic) infants; the Alliance Formation hypothesis, which describes handling as a social commodity and predicts females with infants will support handlers during conflict; and the Learning-to-Mother hypothesis, which describes handling as a mechanism through which handlers learn species-specific maternal behaviors and predicts that handling will occur most frequently in immature and nulliparous females.

Prevalence and characteristics of hair plucking in captive bonobos (Pan paniscus) in North American zoos.

When primates exhibit hair loss and are observed to engage in self or social hair plucking (a rapid jerking away of the hair shaft and follicle by the hand or mouth, often accompanied by inspection, and consumption) the altered appearance, and behavior patterns are thought to reflect individual physiological, and psychological well-being. Hair loss and hair plucking occur in many captive primate species, including all of the great apes. We present the first survey of this behavior among captive bonobos (N = 88; 50 females and 38 males) in seven zoos in the United States.

Laterality of Grooming and Tool Use in a Group of Captive Bonobos (Pan paniscus).

Humans exhibit population level handedness for the right hand; however, the evolution of this behavioral phenotype is poorly understood. Here, we compared the laterality of a simple task (grooming) and a complex task (tool use) to investigate whether increasing task difficulty elicited individual hand preference among a group of captive bonobos (Pan paniscus). Subjects were 17 bonobos housed at the Columbus Zoo and Aquarium.

Hair plucking, stress, and urinary cortisol among captive bonobos (Pan paniscus).

Hair plucking has been observed in many captive primate species, including the great apes; however, the etiology of this behavioral pattern is poorly understood. While this behavior has not been reported in wild apes, an ethologically identical behavior in humans, known as trichotillomania, is linked to chronic psychosocial stress and is a predominantly female disorder. This study examines hair plucking (defined here as a rapid jerking away of the hair shaft and follicle by the hand or mouth, often accompanied by inspection and consumption of the hair shaft and follicle) in a captive group of bonobos (N = 13) at the Columbus Zoo and Aquarium in Columbus, Ohio.