An ancestral genomic sequence that serves as a nucleation site for de novo gene birth

A short non-coding sequence present between the gamma-glutamyltransferase 1 (GGT1) and gamma-glutamyltransferase 5 (GGT5) genes, termed a spacer sequence has been detected in the genomes of Mus musculus, the house mouse and in Philippine tarsier, a primitive ancestral primate. It is highly conserved during primate evolution with certain sequences being totally invariant from mouse to humans. Evidence is presented to show this intergenic sequence serves as a nucleation site for the initiation of diverse genes. We also outline the birth of the human lincRNA gene BCRP3 (BCR activator of RhoGEF and GTPase 3 pseudogene) during primate evolution. The gene developmental process involves sequence initiation, addition of a complex of tandem transposable elements and addition of a segment of another gene. The sequence, initially formed in the Old World Monkeys such as the Rhesus monkey (Macaca mulatta) and the baboon (Papio anubis), develops into different primate genes before evolving into the human BCRP3 gene; it appears to also include trial and error during sequence/gene formation. The protein gene, GGT5 may have also formed by spacer sequence initiation in an ancient ancestor such as zebrafish, but spacer and GGT5 gene sequence drift during evolution produced a divergence that precludes further assessment.

Transcriptome innovations in primates revealed by single-molecule long-read sequencing

Transcriptomic diversity greatly contributes to the fundamentals of disease, lineage-specific biology, and environmental adaptation. However, much of the actual isoform repertoire contributing to shaping primate evolution remains unknown. Here, we combined deep long- and short-read sequencing complemented with mass spectrometry proteomics in a panel of lymphoblastoid cell lines (LCLs) from human, three other great apes, and rhesus macaque, producing the largest full-length isoform catalog in primates to date. Our transcriptomes reveal thousands of novel transcripts, some of them under active translation, expanding and completing the repertoire of primate gene models. Our comparative analyses unveil hundreds of transcriptomic innovations and isoform usage changes related to immune function and immunological disorders. The confluence of these innovations with signals of positive selection and their limited impact in the proteome points to changes in alternative splicing in genes involved in immune response as an important target of recent regulatory divergence in primates.

Enriched sleep environments lengthen lemur sleep duration

Characteristics of the sleep-site are thought to influence the quality and duration of primate sleep, yet only a handful of studies have investigated these links experimentally. Using actigraphy and infrared videography, we quantified sleep in four lemur species (Eulemur coronatus, Lemur catta, Propithecus coquereli, and Varecia rubra) under two different experimental conditions at the Duke Lemur Center (DLC) in Durham, NC, USA. Individuals from each species underwent three weeks of simultaneous testing to investigate the hypothesis that comfort level of the sleep-site influences sleep. We obtained baseline data on normal sleep, and then, in a pair-wise study design, we compared the daily sleep times, inter-daily activity stability, and intra-daily activity variability of individuals in simultaneous experiments of sleep-site enrichment and sleep-site impoverishment. Over 164 24-hour periods from 8 individuals (2 of each species), we found evidence that enriched sleep-sites increased daily sleep times of lemurs, with an average increase of thirty-two minutes. The effect of sleep-site impoverishment was small and not statistically significant. Though our experimental manipulations altered inter-daily stability and intra-daily variability in activity patterns relative to baseline, the changes did not differ significantly between enriched and impoverished conditions. We conclude that properties of a sleep-site enhancing softness or insulation, more than the factors of surface area or stability, influence lemur sleep, with implications regarding the importance of nest building in primate evolution and the welfare and management of captive lemurs.

The Genomic Organization of the LILR Region Remained Largely Conserved Throughout Primate Evolution: Implications for Health And Disease

The genes of the leukocyte immunoglobulin-like receptor (LILR) family map to the leukocyte receptor complex (LRC) on chromosome 19, and consist of both activating and inhibiting entities. These receptors are often involved in regulating immune responses, and are considered to play a role in health and disease. The human LILR region and evolutionary equivalents in some rodent and bird species have been thoroughly characterized. In non-human primates, the LILR region is annotated, but a thorough comparison between humans and non-human primates has not yet been documented. Therefore, it was decided to undertake a comprehensive comparison of the human and non-human primate LILR region at the genomic level. During primate evolution the organization of the LILR region remained largely conserved. One major exception, however, is provided by the common marmoset, a New World monkey species, which seems to feature a substantial contraction of the number of LILR genes in both the centromeric and the telomeric region. Furthermore, genomic analysis revealed that the killer-cell immunoglobulin-like receptor gene KIR3DX1, which maps in the LILR region, features one copy in humans and great ape species. A second copy, which might have been introduced by a duplication event, was observed in the lesser apes, and in Old and New World monkey species. The highly conserved gene organization allowed us to standardize the LILR gene nomenclature for non-human primate species, and implies that most of the receptors encoded by these genes likely fulfill highly preserved functions.

Evolutionary dynamics of circular RNAs in primates

Many primate genes produce circular RNAs (circRNAs). However, the extent of circRNA conservation between closely related species remains unclear. By comparing tissue-specific transcriptomes across over 70 million years of primate evolution, we identify that within 3 million years circRNA expression profiles diverged such that they are more related to species identity than organ type. However, our analysis also revealed a subset of circRNAs with conserved neural expression across tens of millions of years of evolution. By comparing to species-specific circRNAs, we identified that the downstream intron of the conserved circRNAs display a dramatic lengthening during evolution due to the insertion of novel retrotransposons. Our work provides comparative analyses of the mechanisms promoting circRNAs to generate increased transcriptomic complexity in primates.

The Metaphysics of Practical Rationality: Intentional and Deontic Cognition

Despite growing appreciation in recent decades of the importance of shared intentional mental states as a foundation for everything from divergences in primate evolution, to the institution of communal norms, to trends in the development of modernity as a sociopolitical phenomenon, we lack an adequate understanding of the relationship between individual and shared intentionality. At the same time, it is widely appreciated that deontic reasoning concerning what ought, may, and ought not be done is, like reasoning about our intentions, an exercise of practical rationality. Taking advantage of this fact, I use a plan-theoretic semantics for the deontic modalities as a basis for understanding individual and shared intentions. This results in a view that accords well with what we currently have reason to believe about the phylogenetic and ontogenetic development of norm psychology and shared intentionality in human beings, and where original intentionality can be understood in terms of the shared intentionality of a community.

Enriched sleep environments lengthen lemur sleep duration

Characteristics of the sleep-site are thought to influence the quality and duration of primate sleep, yet only a handful of studies have investigated these links experimentally. Using actigraphy and infrared videography, we quantified sleep in four lemur species ( Eulemur coronatus, Lemur catta, Propithecus coquereli, and Varecia rubra ) under two different experimental conditions at the Duke Lemur Center (DLC) in Durham, NC, USA. Individuals from each species underwent three weeks of simultaneous testing to investigate the hypothesis that comfort level of the sleep-site influences sleep. We obtained baseline data on normal sleep, and then, in a pair-wise study design, we compared the daily sleep times of individuals in simultaneous experiments of sleep-site enrichment and sleep-site impoverishment. Over 163 24-hour periods from 8 individuals (2 of each species), we found strong evidence that enriched sleep-sites increased daily sleep times of lemurs, with an average increase of thirty-one minutes. The effect of sleep-site impoverishment was small and not statistically significant. We conclude that properties of a sleep-site enhancing softness or insulation, more than the factors of surface area or stability, influence lemur sleep, with implications regarding the importance of nest building in primate evolution and the welfare and management of captive lemurs.

Glycan-based shaping of the microbiota during primate evolution

Genes encoding glycosyltransferases can be under relatively high selection pressure, likely due to the involvement of the glycans synthesized in host-microbe interactions. Here, we used mice as an experimental model system to investigate whether loss of α−1,3-galactosyltransferase gene (GGTA1) function and Galα1-3Galβ1-4GlcNAcβ1-R (αGal) glycan expression affects host-microbiota interactions, as might have occurred during primate evolution. We found that Ggta1 deletion shaped the composition of the gut microbiota. This occurred via an immunoglobulin (Ig)-dependent mechanism, associated with targeting of αGal-expressing bacteria by IgA. Systemic infection with an Ig-shaped microbiota inoculum elicited a less severe form of sepsis compared to infection with non-Ig-shaped microbiota. This suggests that in the absence of host αGal, antibodies can shape the microbiota towards lower pathogenicity. Given the fitness cost imposed by bacterial sepsis, we infer that the observed reduction in microbiota pathogenicity upon Ggta1 deletion in mice may have contributed to increase the frequency of GGTA1 loss-of-function mutations in ancestral primates that gave rise to humans.