Conservation, evolution, and regulation of splicing during prefrontal cortex development in humans, chimpanzees, and macaques.

Changes in splicing are known to affect the function and regulation of genes. We analyzed splicing events that take place during the postnatal development of the prefrontal cortex in humans, chimpanzees, and rhesus macaques based on data obtained from 168 individuals. Our study revealed that among the 38,822 quantified alternative exons, 15% are differentially spliced among species, and more than 6% splice differently at different ages. Mutations in splicing acceptor and/or donor sites might explain more than 14% of all splicing differences among species and up to 64% of high-amplitude differences. A reconstructed trans-regulatory network containing 21 RNA-binding proteins explains a further 4% of splicing variations within species. While most age-dependent splicing patterns are conserved among the three species, developmental changes in intron retention are substantially more pronounced in humans.

Ultrastructure of Lingual Papillae in Common Chimpanzee (Pan troglodytes) Foetus, Newborn and Adult Specimens.

Among primates, the two recognized species of chimpanzees (common chimpanzee, Pan troglodytes; pygmy chimpanzee, Pan paniscus) are considered to be the most similar to humans. Importantly, in mammals, the food intake behaviour largely determines the tongue morphology, including the type, proportion and distribution of gustatory and non-gustatory tongue papillae. The lingual papillae form during its development and mature in post-natal life depending on the different feeding. In this study, we have used scanning electron microscopy to analyse the age-related changes in the lingual papillae of foetal, newborn and adult P. troglodytes. Four main types of lingual papillae, denominated filiform, fungiform, foliate and vallate, and one subtype of filiform papillae called conical papillae, were found. The main age-related changes observed in all kinds of papillae were a progressive keratinization and morphological complexity along the lifespan. During the foetal period, there was scarce keratinization, which progressively increases in young animals to adulthood. The number of filiform increased with ageing, and both filiform and fungiform papillae in adult tongues are divided into pseudopapillae. On the other hand, the vallate papillae vary from smooth simple surfaces in foetal tongues to irregular surfaces with grooves and pseudopapillae (microscopic papilla-shaped formations within the papilla itself) in adults. These results describe for the first time the age-related variations in the three-dimensional aspect of lingual papillae of the chimpanzee tongue and provide new data to characterize more precisely these structures in the human closest specie.

Development of Modular Organization in the Chimpanzee Pelvis.

The bony pelvis of primates is a composite structure serving a variety of functions, and exhibiting a complex pattern of modularity and integration. Still little is known, however, about how patterns of modularity and integration arise, and how they change throughout ontogeny. Here we study the ontogeny of modularity and integration in developmental and functional units of the pelvis of our closest living relatives, the chimpanzees. We use methods of biomedical imaging and geometric morphometrics to quantify pelvic shape change from late fetal stages to adulthood, and to track changes in patterns of covariation within and among pelvic regions. Our results show that both developmental and functional units of the pelvis exhibit significant levels of modularity throughout ontogeny. Modularity of developmental units (ilium, ischium, and pubis) decreases with increasing age, whereas modularity of functional units tends to increase. We suggest that the decreasing modularity and increasing integration of developmental units reflects their gradual fusion. In contrast, increasing modularity of functional pelvic units likely reflects changing functional demands during an individual's lifetime. Overall, ontogenetic changes in patterns of modularity and integration imply that natural selection could act differently on each module, either developmental or functional, at different stages of ontogeny. This further implies that adult patterns of covariation in the pelvis provide only limited information about its evolvability. Anat Rec, 300:675-686, 2017. © 2017 Wiley Periodicals, Inc.

Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series.

BACKGROUND: Comparing biological time series data across different conditions, or different specimens, is a common but still challenging task. Algorithms aligning two time series represent a valuable tool for such comparisons. While many powerful computation tools for time series alignment have been developed, they do not provide significance estimates for time shift measurements. RESULTS: Here, we present an extended version of the original DTW algorithm that allows us to determine the significance of time shift estimates in time series alignments, the DTW-Significance (DTW-S) algorithm. The DTW-S combines important properties of the original algorithm and other published time series alignment tools: DTW-S calculates the optimal alignment for each time point of each gene, it uses interpolated time points for time shift estimation, and it does not require alignment of the time-series end points. As a new feature, we implement a simulation procedure based on parameters estimated from real time series data, on a series-by-series basis, allowing us to determine the false positive rate (FPR) and the significance of the estimated time shift values. We assess the performance of our method using simulation data and real expression time series from two published primate brain expression datasets. Our results show that this method can provide accurate and robust time shift estimates for each time point on a gene-by-gene basis. Using these estimates, we are able to uncover novel features of the biological processes underlying human brain development and maturation. CONCLUSIONS: The DTW-S provides a convenient tool for calculating accurate and robust time shift estimates at each time point for each gene, based on time series data. The estimates can be used to uncover novel biological features of the system being studied. The DTW-S is freely available as an R package TimeShift at http://www.picb.ac.cn/Comparative/data.html.

Human-specific transcriptional regulation of CNS development genes by FOXP2.

The signalling pathways controlling both the evolution and development of language in the human brain remain unknown. So far, the transcription factor FOXP2 (forkhead box P2) is the only gene implicated in Mendelian forms of human speech and language dysfunction. It has been proposed that the amino acid composition in the human variant of FOXP2 has undergone accelerated evolution, and this two-amino-acid change occurred around the time of language emergence in humans. However, this remains controversial, and whether the acquisition of these amino acids in human FOXP2 has any functional consequence in human neurons remains untested. Here we demonstrate that these two human-specific amino acids alter FOXP2 function by conferring differential transcriptional regulation in vitro. We extend these observations in vivo to human and chimpanzee brain, and use network analysis to identify novel relationships among the differentially expressed genes. These data provide experimental support for the functional relevance of changes in FOXP2 that occur on the human lineage, highlighting specific pathways with direct consequences for human brain development and disease in the central nervous system (CNS). Because FOXP2 has an important role in speech and language in humans, the identified targets may have a critical function in the development and evolution of language circuitry in humans.

Fetal ultrasonography: biometric data from four African primate species.

BACKGROUND: Nonhuman primates are raised in large numbers in research centers and zoos. Reproductive monitoring is required to improve breeding performances. Ultrasonography is a safe method to determine gestational age and to estimate the date of parturition. However only few data are available in nonhuman primates. METHODS: Fetal biometric data were obtained throughout pregnancy on four African primate species, namely chimpanzee, gorilla, mandrill and patas monkey. Measurements included biparietal diameter, transverse abdominal diameter, femur and humerus length, external interorbital diameter, and fetal heart rate. Curves established from these data were compared with previously published data in chimpanzees and gorillas and with those for humans and other closely related primate species. RESULTS: The curves for the different hominids were very similar, while those for mandrills more closely resembled baboons and data for patas monkeys were comparable to those for macaques. CONCLUSIONS: These data, by providing a tool to evaluate precise gestational age, will be useful for centers raising these four primate species.

The nasopalatine duct and the nasal floor cartilages in catarrhine primates.

The nasal floor structures in catarrhine primates have been studied on the basis of histological serial sections of older fetuses of Presbytis, Hylobates, Gorilla, Pan, Pongo and Homo. For outgroup comparisons, sections of the strepsirhine Daubentonia and the platyrrhine Callimico are presented; in these taxa the nasal floor cartilages are intimately connected not only with the nasopalatine duct (STENO) but also with the persisting vomeronasal organ (JACOBSON). Whereas the vomeronasal organ has disappeared as a functioning sensory organ in catarrhines (occasional embryonic vestiges are reported), the nasopalatine duct is retained in cercopithecoids, hylobatids and in Gorilla; in Pan, Pongo and Homo at least remnants of the duct and of the associated cartilages are preserved. The systematic meanings of these findings have been discussed.

[Spatial distribution of facial volumes. Ontogenetic and phylogenetic study with vestibular orientation]. / Répartition spatiale des volumes faciaux. Etude ontogénique et phylogénique en orientation vestibulaire.

On cephalic skeleton of Man and two species of chimpanzees, statistically considered during their growing, a sagittal area is measured in facial mass and total face. Barycenters are determined. This points describe, in vestibular axis, ontogenic curves with posterior concavity more important in Man. Remarkable relations exist between barycenters and several facial and mandibular points, and with those of frontal and parietal vault.

Appearance of ossification centers of the lower arm, wrist, lower leg, and ankle in immature orangutans and chimpanzees with an assessment of the relationship of ossification to dental development.

This study examines the appearance of the secondary ossification centers in the lower arms, wrists, lower legs, and ankles of a cross-sectional sample of 20 infant orangutans and chimpanzees (15 of known age). The number of tarsal and carpal centers is analyzed relative to the degree of M1 development and the weight of individual animals. Variation in the appearance of these ossification centers is discussed relative to these variables and others. In addition, a sequence of appearance is established for the carpal and tarsal ossification centers in the orangutan and data is presented on the status of these centers in a fetal and newborn gorilla. Study results indicate that 1) there is variation in the number of secondary epiphyses present in animals of similar ages; 2) tarsal ossification is completed prior to carpal ossification in the orangutan; 3) there are indications of a relationship between weight and the number of ossification centers present in animals of similar age; and 4) there appears to be no evidence of specific relationships between carpal and tarsal development and M1 development.