Primate evolution - in and out of Africa

Reanalysis of Samburupithecus reveals similarities to nyanzapithecines

Samburupithecus kiptalami is an ape found in Late Miocene deposits (ca. 9.5 Ma) of northern Kenya. Initial assessments of the holotype specimen (KNM-SH 8531), a female-gorilla-sized maxillary fragment preserving the postcanine tooth row, noted similarities to gorillas or to African apes more broadly. More recently, primitive features of the maxilla and dentition have been used to propose a stem hominoid position for Samburupithecus. In particular, Samburupithecus shares some dental features with orepithecids (nyanzapithecines and Oreopithecus). To evaluate these competing hypotheses, and investigate possible affinities to oreopithecids, we reanalyzed the dentition of Samburupithecus quantitatively and assessed qualitative dental and maxillary features shared by oreopithecids and Samburupithecus. Based on the results of our analyses, we suggest that Samburupithecus is a late-occurring African oreopithecid, which we regard as a long-lived family of stem hominoids. The inclusion of Samburupithecus within Oreopithecidae highlights that stem hominoids and oreopithecids, in particular, spanned a large range of body sizes, similar to the range of size variation seen among all extant apes. Finally, the presence of oreopithecids in Africa on either side of a notable gap in the Late Miocene African fossil record of apes (from ∼13 to 10 Ma) demonstrates that the rarity of fossil African apes (i.e., nonhominin hominines) during this period is likely due to sampling biases rather than a recent immigration back into Africa from Eurasia.

Sequence Analysis of microRNAs Encoded by Simian Lymphocryptoviruses

Lymphocryptoviruses (LCVs) are ubiquitous gamma-herpesviruses that establish life-long infections in both humans and non-human primates (NHPs). In immunocompromised hosts, LCV infections are commonly associated with B cell disorders and malignancies such as lymphoma. In this study, we evaluated simian LCV-encoded small microRNAs (miRNAs) present in lymphoblastoid cell lines (LCLs) derived from a Mauritian cynomolgus macaque (Macaca fascicularis) with cyLCV-associated post-transplant lymphoproliferative disease (PTLD) as well as the viral miRNAs expressed in a baboon (Papio hamadryas) LCL that harbors CeHV12. Via sequence comparisons, we further predicted viral miRNAs encoded by LCVs that infect two additional NHP species: stump-tailed macaques (Macaca arctoides) and bonobos (Pan paniscus). Together, these species represent two arms of the primate phylogeny: Hominoids (Pan) and Old-World monkeys (Macaca, Papio). Through our analysis, we defined sequences for >95 viral miRNAs encoded by these four NHP LCVs. Our study provides the most comprehensive annotation of NHP LCV miRNAs to date, yielding a resource for developing sequence-specific reagents to detect these molecules. Importantly, we further demonstrate that cyLCV miRNAs can be detected in circulation in vivo and have biomarker potential for LCV-related PTLD.

Understanding the heterogeneity of anxiety using a translational neuroscience approach

Anxiety disorders affect millions of people worldwide and present a challenge in neuroscience research because of their substantial heterogeneity in clinical presentation. While a great deal of progress has been made in understanding the neurobiology of fear and anxiety, these insights have not led to effective treatments. Understanding the relationship between phenotypic heterogeneity and the underlying biology is a critical first step in solving this problem. We show translation, reverse translation, and computational modeling can contribute to a refined, cross-species understanding of fear and anxiety as well as anxiety disorders. More specifically, we outline how animal models can be leveraged to develop testable hypotheses in humans by using targeted, cross-species approaches and ethologically informed behavioral paradigms. We discuss reverse translational approaches that can guide and prioritize animal research in nontraditional research species. Finally, we advocate for the use of computational models to harmonize cross-species and cross-methodology research into anxiety. Together, this translational neuroscience approach will help to bridge the widening gap between how we currently conceptualize and diagnose anxiety disorders, as well as aid in the discovery of better treatments for these conditions.

"ATAD3C regulates ATAD3A assembly and function in the mitochondrial membrane"

Mitochondrial ATAD3A is an ATPase Associated with diverse cellular Activities (AAA) domain containing enzyme, involved in the structural organization of the inner mitochondrial membrane and of increasing importance in childhood disease. In humans, two ATAD3A paralogs arose by gene duplication during evolution: ATAD3B and ATAD3C. Here we investigate the cellular activities of the ATAD3C paralog that has been considered a pseudogene. We detected unique ATAD3C peptides in HEK 293T cells, with expression similar to that in human tissues, and showed that it is an integral membrane protein that exposes its carboxy-terminus to the intermembrane space. Overexpression of ATAD3C, but not of ATAD3A, in fibroblasts caused a decrease in cell proliferation and oxygen consumption rate, and an increase of cellular ROS. This was due to the incorporation of ATAD3C monomers in ATAD3A complex in the mitochondrial membrane reducing its size. Consistent with a negative regulation of ATAD3A function in mitochondrial membrane organization, ATAD3C expression led to increased accumulation of respiratory chain dimeric CIII in the inner membrane, to the detriment to that assembled in respiratory supercomplexes. Our results demonstrate a negative dominant role of the ATAD3C paralog with implications for mitochondrial OXPHOS function and suggest that its expression regulates ATAD3A in the cell.

Landscape genomics analysis provides insights into future climate change-driven risk in rhesus macaque

Climate change significantly affects the suitability of wildlife habitats. Thus, understanding how animals adapt ecologically and genetically to climate change is important for targeted species protection. Rhesus macaques (Macaca mulatta) are widely distributed and multi-climatically adapted primates. This study explored how rhesus macaques adapt to climate change by integrating ecological and genetic methods and applying species distribution models (SDMs) and a gradient forest (GF) model. The findings suggested that temperature seasonality primarily affects habitat suitability and indicated that climate change will have a dramatic impact on macaque populations in the future. We also applied genotype-environment association (GEA) analyses and selection signature analyses to identify genes associated with climate change and provide possible explanations for the adaptation of rhesus macaques to climatic environments. The population genomics analyses suggested that the Taihang population has the highest genomic vulnerability with inbreeding and low heterozygosity. Combined with the higher ecological vulnerability, additional conservation strategies are required for this population under higher risk of climate change. Our work measured the impact of climate change and enabled the identification of populations that exhibit high vulnerability to severe climate change. Such information is useful for selecting populations of rhesus macaques as subject of long-term monitoring or evolutionary rescue under future climate change.

An Evolutionary Model for the Ancient Origins of Polycystic Ovary Syndrome

Polycystic ovary syndrome (PCOS) is a common endocrinopathy of reproductive-aged women, characterized by hyperandrogenism, oligo-anovulation and insulin resistance and closely linked with preferential abdominal fat accumulation. As an ancestral primate trait, PCOS was likely further selected in humans when scarcity of food in hunter-gatherers of the late Pleistocene additionally programmed for enhanced fat storage to meet the metabolic demands of reproduction in later life. As an evolutionary model for PCOS, healthy normal-weight women with hyperandrogenic PCOS have subcutaneous (SC) abdominal adipose stem cells that favor fat storage through exaggerated lipid accumulation during development to adipocytes in vitro. In turn, fat storage is counterbalanced by reduced insulin sensitivity and preferential accumulation of highly lipolytic intra-abdominal fat in vivo. This metabolic adaptation in PCOS balances energy storage with glucose availability and fatty acid oxidation for optimal energy use during reproduction; its accompanying oligo-anovulation allowed PCOS women from antiquity sufficient time and strength for childrearing of fewer offspring with a greater likelihood of childhood survival. Heritable PCOS characteristics are affected by today's contemporary environment through epigenetic events that predispose women to lipotoxicity, with excess weight gain and pregnancy complications, calling for an emphasis on preventive healthcare to optimize the long-term, endocrine-metabolic health of PCOS women in today's obesogenic environment.

Tropomyosin Isoform Diversity in the Cynomolgus Monkey Heart and Skeletal Muscles Compared to Human Tissues

Old world monkeys separated from the great apes, including the ancestor of humans, about 25 million years ago, but most of the genes in humans and various nonhuman primates are quite similar even though their anatomical appearances are quite different. Like other mammals, primates have four tropomyosin genes (TPM1, TPM2, TPM3, and TPM4) each of which generates a multitude of TPM isoforms via alternative splicing. Only TPM1 produces two sarcomeric isoforms (TPM1α and TPM1κ), and TPM2, TPM3, and TPM4 each generate one sarcomeric isoform. We have cloned and sequenced TPM1α, TPM1κ, TPM2α, TPM3α, and TPM4α with RNA from cynomolgus (Cyn) monkey hearts and skeletal muscle. We believe this is the first report of directly cloning and sequencing of these monkey transcripts. In the Cyn monkey heart, the rank order of TPM isoform expression is TPM1α > TPM2α > TPM1κ > TPM3α > TPM4α. In the Cyn monkey skeletal muscle, the rank order of expression is TPM1α > TPM2α > TPM3α > TPM1κ > TPM4α. The major differences in the human heart are the increased expression of TPM1κ, although TPM1α is still the dominant transcript. In the Cyn monkey heart, the only sarcomeric TPM isoform at the protein level is TPM1α. This is in contrast to human hearts where TPM1α is the major sarcomeric isoform but a lower quantity of TPM1κ, TPM2α, and TPM3α is also detected at the protein level. These differences of tropomyosin and/or other cardiac protein expression in human and Cyn monkey hearts may reflect the differences in physiological activities in daily life.

Investigation of white matter and grey matter alteration in the monkey brain following ischemic stroke by using diffusion tensor imaging

Background

Investigation of stroke lesion has mostly focused on grey matter (GM) in previous studies and white matter (WM) degeneration during acute stroke is understudied. In the present study, monkeys were utilized to investigate the alterations of GM and WM in the brain following ischemic occlusion using diffusion tensor imaging (DTI).

Methods

Permanent middle cerebral artery occlusion (pMCAO) was induced in rhesus monkeys (n=6) with an interventional approach. Serial DTI was conducted on a clinical 3T in the hyperacute phase (2-6 hours), 48, and 96 hours post occlusion. Regions of interest in GM and WM of lesion areas were selected for data analysis.

Results

Mean diffusivity (MD), radial diffusivity (RD), and axial Diffusivity (AD) in WM decreased substantially during hyperacute stroke, as similar as those seen in GM. No obvious fractional anasotropy (FA) changes were seen in GM and WM during hyper acute phase. until 48 hours post stroke when significant fiber losses were oberved also. Pseudo-normalization of MD, AD, and RD was seen at 96 hours. Pathological changes of WM and GM were observed in ischemic areas at 8, 48, and 96 hours post stroke. Relative changes of MD, AD and RD of WM were correlated negatively with infarction volumes at 6 hours post stroke.

Conclusion

The present study revealed the microstructural changes in gray matter and white matter of monkey brains during acute stroke by using DTI. The preliminary results suggest axial and radial diffusivity (AD and RD) may be sensitive surrogate markers to assess specific microstructural changes in white matter during hyper-acute stroke.

Magnetic resonance imaging of the monkey fetal brain in utero

Non-human primates (NHPs) are the closest living relatives of the human and play a critical role in investigating the effects of maternal viral infection and consumption of medicines, drugs, and alcohol on fetal development. With the advance of contemporary fast MRI techniques with parallel imaging, fetal MRI is becoming a robust tool increasingly used in clinical practice and preclinical studies to examine congenital abnormalities including placental dysfunction, congenital heart disease (CHD), and brain abnormalities non-invasively. Because NHPs are usually scanned under anesthesia, the motion artifact is reduced substantially, allowing multi-parameter MRI techniques to be used intensively to examine the fetal development in a single scanning session or longitudinal studies. In this paper, the MRI techniques for scanning monkey fetal brains in utero in biomedical research are summarized. Also, a fast imaging protocol including T2-weighted imaging, diffusion MRI, resting-state functional MRI (rsfMRI) to examine rhesus monkey fetal brains in utero on a clinical 3T scanner is introduced.

Young children spontaneously invent three different types of associative tool use behaviour

Associative Tool Use (ATU) describes the use of two or more tools in combination, with the literature further differentiating between Tool set use, Tool composite use, Sequential tool use and Secondary tool use. Research investigating the cognitive processes underlying ATU has shown that some primate and bird species spontaneously invent Tool set and Sequential tool use. Yet studies with humans are sparse. Whether children are also able to spontaneously invent ATU behaviours and at what age this ability emerges is poorly understood. We addressed this gap in the literature with two experiments involving preschoolers (E1, N = 66, 3 years 6 months to 4 years 9 months; E2, N = 119, 3 years 0 months to 6 years 10 months) who were administered novel tasks measuring Tool set, Metatool and Sequential tool use. Participants needed to solve the tasks individually, without the opportunity for social learning (except for enhancement effects). Children from 3 years of age spontaneously invented all of the types of investigated ATU behaviours. Success rates were low, suggesting that individual invention of ATU in novel tasks is still challenging for preschoolers. We discuss how future studies can use and expand our tasks to deepen our understanding of tool use and problem-solving in humans and non-human animals.

Understanding COVID-19: From Dysregulated Immunity to Vaccination Status Quo

The development of vaccines against infectious diseases has helped us battle the greatest threat to public health. With the emergence of novel viruses, targeted immunotherapeutics ranging from informed vaccine development to personalized medicine may be the very thing that separates us between life and death. Late in 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of coronavirus disease 2019 (COVID-19), made a remarkable entrance to human civilization, being one of many to cross the species barrier. This review discusses the important aspects of COVID-19, providing a brief overview of our current understanding of dysregulated immune responses developed using various experimental models, a brief outline of experimental models of COVID-19 and more importantly, the rapid development of vaccines against COVID-19.

Greater dependence on working memory and restricted familiarity in orangutans compared with rhesus monkeys

The prefrontal cortex is larger than would be predicted by body size or visual cortex volume in great apes compared with monkeys. Because prefrontal cortex is critical for working memory, we hypothesized that recognition memory tests would engage working memory in orangutans more robustly than in rhesus monkeys. In contrast to working memory, the familiarity response that results from repetition of an image is less cognitively taxing and has been associated with nonfrontal brain regions. Across three experiments, we observed a striking species difference in the control of behavior by these two types of memory. First, we found that recognition memory performance in orangutans was controlled by working memory under conditions in which this memory system plays little role in rhesus monkeys. Second, we found that unlike the case in monkeys, familiarity was not involved in recognition memory performance in orangutans, shown by differences with monkeys across three different measures. Memory in orangutans was not improved by use of novel images, was always impaired by a concurrent cognitive load, and orangutans did not accurately identify images seen minutes ago. These results are surprising and puzzling, but do support the view that prefrontal expansion in great apes favored working memory. At least in orangutans, increased dependence on working memory may come at a cost in terms of the availability of familiarity.

Application of a novel haplotype-based scan for local adaptation to study high-altitude adaptation in rhesus macaques

When natural populations split and migrate to different environments, they may experience different selection pressures that can lead to local adaptation. To capture the genomic patterns of a local selective sweep, we develop XP-nSL, a genomic scan for local adaptation that compares haplotype patterns between two populations. We show that XP-nSL has power to detect ongoing and recently completed hard and soft sweeps, and we then apply this statistic to search for evidence of adaptation to high altitude in rhesus macaques. We analyze the whole genomes of 23 wild rhesus macaques captured at high altitude (mean altitude > 4000 m above sea level) to 22 wild rhesus macaques captured at low altitude (mean altitude < 500 m above sea level) and find evidence of local adaptation in the high-altitude population at or near 303 known genes and several unannotated regions. We find the strongest signal for adaptation at EGLN1, a classic target for convergent evolution in several species living in low oxygen environments. Furthermore, many of the 303 genes are involved in processes related to hypoxia, regulation of ROS, DNA damage repair, synaptic signaling, and metabolism. These results suggest that, beyond adapting via a beneficial mutation in one single gene, adaptation to high altitude in rhesus macaques is polygenic and spread across numerous important biological systems.

The germline mutational process in rhesus macaque and its implications for phylogenetic dating

BACKGROUND

Understanding the rate and pattern of germline mutations is of fundamental importance for understanding evolutionary processes.

RESULTS

Here we analyzed 19 parent-offspring trios of rhesus macaques (Macaca mulatta) at high sequencing coverage of ∼76× per individual and estimated a mean rate of 0.77 × 10-8de novo mutations per site per generation (95% CI: 0.69 × 10-8 to 0.85 × 10-8). By phasing 50% of the mutations to parental origins, we found that the mutation rate is positively correlated with the paternal age. The paternal lineage contributed a mean of 81% of the de novo mutations, with a trend of an increasing male contribution for older fathers. Approximately 3.5% of de novo mutations were shared between siblings, with no parental bias, suggesting that they arose from early development (postzygotic) stages. Finally, the divergence times between closely related primates calculated on the basis of the yearly mutation rate of rhesus macaque generally reconcile with divergence estimated with molecular clock methods, except for the Cercopithecoidea/Hominoidea molecular divergence dated at 58 Mya using our new estimate of the yearly mutation rate.

CONCLUSIONS

When compared to the traditional molecular clock methods, new estimated rates from pedigree samples can provide insights into the evolution of well-studied groups such as primates.

Taxonomic Revision and Evolutionary Phylogeography of Dusky Langur (Trachypithecus obscurus) in Peninsular Malaysia

Dusky langur, Trachypithecus obscurus, inhabits tropical rainforests in Peninsular Malaysia, Thailand, and Myanmar. Morphologically, five subspecies are distributed in Peninsular Malaysia, but few studies have used genetic data to verify the classification. It is difficult to differentiate subspecies based on morphological characteristics, so this study used molecular data to differentiate subspecies of T. obscurus. The issue was addressed by analyzing 723 and 649 base pairs of the mitochondrial D-loop region and COI, respectively. DNA amplifications were performed using species-specific primer toward 35 individuals representing different populations. Phylogenetic analyses showed that two main clades representing populations in southern and northern Peninsular Malaysia. The results demonstrate that subspecies of T. obscurus in Peninsular Malaysia does not support classification based on the morphology that recognizes five subspecies. Previous study based on morphology that classified the subspecies on Perhentian Island, Terengganu, as T. obscurus styx is not recognized in this study. This subspecies happened to merge with the population in northern Peninsular Malaysia. Trachypithecus o. styx probably inhabited the southern peninsula and, due to the terminal Pleistocene sea level rise, spread to the east coast but could not spread farther because the subspecies was situated on offshore islands during the period. This assumption was supported by the molecular clock, which showed that subspecies on Perhentian Island spread after the Perlis population (T. obscurus flavicauda).

Macaques in China: Evolutionary dispersion and subsequent development

Depicting a taxonomic group's evolutionary trajectory as a function of changes in the geographical landscape and its historical distribution is critical for constructing informed conservation strategies. Based on fossil sites from the Pliocene to the Holocene, and historical records since 1175 AD, we established macaques’ dispersal pathways into and through China. These routes include internal pathways starting from the southeast corner of the Qinghai‐Tibet Plateau and Mts. Hengduan in western China, and the routes through the estuaries of the three major rivers (Yangtze, Yellow, and Pearl). Our results indicate that macaques used the three rivers and avoided the higher elevation of the plateaus to promote their radiation. They occupied the whole mainland and islands in the Pleistocene and experienced shrunken distribution in the Holocene due to climate changes and human‐induced activities. A prominent China‐wide reduction occurred between 1817 and 1917; and a remarkable retraction from central China happened between 1918 and 2018 following further eco‐social development and human expansion in central China, particularly since the second half of the last century. Starting in 1175 there was a restriction of range to higher altitudes, so that macaques have contracted their range to the west, and the Qinghai‐Tibet Plateau and Mts. Hengduan have become an important sanctuary. We predict that if the current climate and human‐induced changes are not reversed by decisive conservation actions, macaques in east and central China will likely be extinct in the near future.

Major waterways used by the primates to disperse and radiate in China

Primate evolution and dispersion in East Asia from the Pliocene to the Early Holocene

Historically shrunk macaque distribution in China

A cross-cultural investigation of young children's spontaneous invention of tool use behaviours

Through the mechanisms of observation, imitation and teaching, young children readily pick up the tool using behaviours of their culture. However, little is known about the baseline abilities of children's tool use: what they might be capable of inventing on their own in the absence of socially provided information. It has been shown that children can spontaneously invent 11 of 12 candidate tool using behaviours observed within the foraging behaviours of wild non-human apes (Reindl et al. 2016 Proc. R. Soc. B 283, 20152402. (doi:10.1098/rspb.2015.2402)). However, no investigations to date have examined how tool use invention in children might vary across cultural contexts. The current study investigated the levels of spontaneous tool use invention in 2- to 5-year-old children from San Bushmen communities in South Africa and children in a large city in Australia on the same 12 candidate problem-solving tasks. Children in both cultural contexts correctly invented all 12 candidate tool using behaviours, suggesting that these behaviours are within the general cognitive and physical capacities of human children and can be produced in the absence of direct social learning mechanisms such as teaching or observation. Children in both cultures were more likely to invent those tool behaviours more frequently observed in great ape populations than those less frequently observed, suggesting there is similarity in the level of difficulty of invention across these behaviours for all great ape species. However, children in the Australian sample invented tool behaviours and succeeded on the tasks more often than did the Bushmen children, highlighting that aspects of a child's social or cultural environment may influence the rates of their tool use invention on such task sets, even when direct social information is absent.

Evolution of the bitter taste receptor TAS2R38 in colobines

Bitter taste perception enables the detection of potentially toxic molecules and thus evokes avoidance behavior in vertebrates. It is mediated by bitter taste receptors, TAS2Rs. One of the best-studied TAS2R is TAS2R38. Phenylthiocarbamide (PTC) perception and TAS2R38 receptors vary across primate species, and this variation may be related to variation in dietary preferences. In particular, we previously found that the low sensitivity of TAS2R38s in Asian colobines likely evolved as an adaptation to their leaf-eating behavior. However, it remains unclear whether this low PTC sensitivity is a general characteristic of the subfamily Colobinae, a primate group that feeds predominantly on leaves. We performed genetic analyses, functional assays with mutant proteins, and behavioral analyses to evaluate the general characteristics of TAS2R38 in colobines. We found that PTC sensitivity is lower in TAS2R38s of African colobines than in TAS2R38s of omnivorous macaques. Furthermore, two amino acids shared between Asian and African colobines were responsible for low sensitivity to PTC, suggesting that the last common ancestor of extant colobines had this phenotype. We also detected amino acid differences between TAS2R38s in Asian and African colobines, indicating that they evolved independently after the separation of these groups.

Defining the ecological and evolutionary drivers of Plasmodium knowlesi transmission within a multi-scale framework

Plasmodium knowlesi is a zoonotic malaria parasite normally residing in long-tailed and pig-tailed macaques (Macaca fascicularis and Macaca nemestrina, respectively) found throughout Southeast Asia. Recently, knowlesi malaria has become the predominant malaria affecting humans in Malaysian Borneo, being responsible for approximately 70% of reported cases. Largely as a result of anthropogenic land use changes in Borneo, vectors which transmit the parasite, along with macaque hosts, are both now frequently found in disturbed forest habitats, or at the forest fringes, thus having more frequent contact with humans. Having access to human hosts provides the parasite with the opportunity to further its adaption to the human immune system. The ecological drivers of the transmission and spread of P. knowlesi are operating over many different spatial (and, therefore, temporal) scales, from the molecular to the continental. Strategies to prevent and manage zoonoses, such as P. knowlesi malaria require interdisciplinary research exploring the impact of land use change and biodiversity loss on the evolving relationship between parasite, reservoir hosts, vectors, and humans over multiple spatial scales.

Proteomic Analysis of Baboon Cerebral Artery Reveals Potential Pathways of Damage by Prenatal Alcohol Exposure

Alcohol is one of the most widely misused substances in the world. Alcohol consumption by pregnant women often results in an array of fetal developmental abnormalities, but the damage to the fetus by alcohol remains poorly understood. The limited knowledge regarding the molecular targets of alcohol in the developing fetus constitutes one of the major obstacles in developing effective pharmacological interventions that could prevent fetal damage after alcohol consumption by pregnant women. The fetal cerebral artery is emerging as an important mediator of fetal cerebral damage by maternal alcohol drinking. In the present work, we conduct proteomics analysis of cerebral (basilar) artery lysates of near-term fetal baboons to search for protein targets of fetal alcohol exposure. Our study demonstrates that 3 episodes of binge alcohol exposure during the second trimester-equivalent of human pregnancy are sufficient to render profound changes in fetal cerebral artery proteome. These changes persisted, as they were detected in near-term fetuses. In particular, the relative abundance of 238 proteins differed significantly between control and alcohol-exposed fetuses. Enrichment analysis pointed at the group of metabolic activity proteins as a major class targeted by alcohol. Western blotting confirmed upregulation of the aldehyde dehydrogenase 6 family member A1 (ALDH6A1) in cerebral artery lysates from alcohol-exposed fetuses. This upregulation translated to greater ALDH activity of cerebral artery lysate of near-term fetuses following prenatal alcohol exposure when compared with controls.

Large conductance voltage- and calcium-gated potassium channels (BK) in cerebral artery myocytes of perinatal fetal primates share several major characteristics with the adult phenotype

Large conductance voltage- and calcium-gated channels (BK) control fundamental processes, including smooth muscle contractility and artery diameter. We used a baboon (Papio spp) model of pregnancy that is similar to that of humans to characterize BK channels in the middle cerebral artery and its branches in near-term (165 dGa) primate fetuses and corresponding pregnant mothers. In cell-attached patches (K+pipette = 135 mM) on freshly isolated fetal cerebral artery myocytes, BK currents were identified by large conductance, and voltage- and paxilline-sensitive effects. Their calcium sensitivity was confirmed by a lower Vhalf (transmembrane voltage needed to reach half-maximal current) in inside-out patches at 30 versus 3 μM [Ca2+]free. Immunostaining against the BK channel-forming alpha subunit revealed qualitatively similar levels of BK alpha protein-corresponding fluorescence in fetal and maternal myocytes. Fetal and maternal BK currents recorded at 3 μM [Ca2+]free from excised membrane patches had similar unitary current amplitude, and Vhalf. However, subtle differences between fetal and maternal BK channel phenotypes were detected in macroscopic current activation kinetics. To assess BK function at the organ level, fetal and maternal artery branches were pressurized in vitro at 30 mmHg and probed with the selective BK channel blocker paxilline (1 μM). The degree of paxilline-induced constriction was similar in fetal and maternal arteries, yet the constriction of maternal arteries was achieved sooner. In conclusion, we present a first identification and characterization of fetal cerebral artery BK channels in myocytes from primates. Although differences in BK channels between fetal and maternal arteries exist, the similarities reported herein advance the idea that vascular myocyte BK channels are functional near-term, and thus may serve as pharmacological targets during the perinatal-neonatal period.

Characteristics of Gorilla-Specific Lactobacillus Isolated from Captive and Wild Gorillas

Lactic acid bacteria (LAB) reside in a wide range of mammals, such as autochthonous intestinal bacteria. In this paper, we present the phenotypic and phylogenetic characteristics of gorilla-specific LAB. Lactobacillus gorillae—previously isolated from the wild and captive western lowland gorillas (Gorilla gorilla gorilla)—were successfully isolated from wild mountain gorillas (Gorilla gorilla beringei) in addition to other captive and wild western lowland gorillas. The strains from wild gorillas could ferment D-xylose, arbutine, cellobiose, and trehalose better than those from captive gorillas. By contrast, tolerance to NaCl was higher in isolates from captive gorillas than in those from wild gorillas. This tendency may have been induced by regular foods in zoos, which contain sufficient amount of salts but less amount of indigestible fiber and plant secondary metabolites compared to foods in the wild. All strains of L. gorillae showed inhibitory activities to enteric pathogenic bacteria; however, the activity was significantly higher for strains from wild gorillas than for those from captive gorillas. This may have been induced by the captive condition with routine veterinary intervention. Since L. gorillae can grow in the gastrointestinal tract of gorillas in captivity, the strains from wild mountain gorillas are potential probiotics for gorillas under captive conditions.

Divergent Solutions to Visual Problem Solving across Mammalian Species

Our understanding of the neurobiological underpinnings of learning and behavior relies on the use of invasive techniques, which necessitate the use of animal models. However, when different species learn the same task, to what degree are they actually producing the same behavior and engaging homologous neural circuitry? This question has received virtually no recent attention, even as the most powerful new methodologies for measuring and perturbing the nervous system have become increasingly dependent on the use of murine species. Here, we test humans, rats, monkeys, and an evolutionarily intermediate species, tree shrews, on a three alternative, forced choice, visual contrast discrimination task. As anticipated, learning rate, peak performance, and transfer across contrasts was lower in the rat compared to the other species. More interestingly, rats exhibited two major behavioral peculiarities: while monkeys and tree shrews based their choices largely on visual information, rats tended to base their choices on past reward history. Furthermore, as the task became more difficult, rats largely disengaged from the visual stimulus, reverting to innate spatial predispositions in order to collect rewards near chance probability. Our findings highlight the limitation of muridae as models for translational research, at least in the area of visually based decision making.

Fetal Cerebral Circulation as Target of Maternal Alcohol Consumption

Alcohol (ethanol [EtOH]) is one of the most widely used psychoactive substances worldwide. Alcohol consumption during pregnancy may result in a wide range of morphological and neurodevelopmental abnormalities termed fetal alcohol spectrum disorders (FASD), with the most severe cases diagnosed as fetal alcohol syndrome (FAS). FAS and FASD are not readily curable and currently represent the leading preventable causes of birth defect and neurodevelopmental delay in the United States. The etiology of FAS/FASD remains poorly understood. This review focuses on the effects of prenatal alcohol exposure (PAE) on fetal cerebrovascular function. A brief introduction to the epidemiology of alcohol consumption and the developmental characteristics of fetal cerebral circulation is followed by several sections that discuss current evidence documenting alcohol-driven alterations of fetal cerebral blood flow, artery function, and microvessel networks. The material offers mechanistic insights at the vascular level itself into the pathophysiology of PAE.

Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey Species

Both diet and host phylogeny shape the gut microbial community, and separating out the effects of these variables can be challenging. In this study, high-throughput sequencing was used to evaluate the impact of diet and phylogeny on the gut microbiota of nine colobine monkey species (N = 64 individuals). Colobines are leaf-eating monkeys that fare poorly in captivity-often exhibiting gastrointestinal (GI) problems. This study included eight Asian colobines (Rhinopithecus brelichi, Rhinopithecus roxellana, Rhinopithecus bieti, Pygathrix nemaeus, Nasalis larvatus, Trachypithecus francoisi, Trachypithecus auratus, and Trachypithecus vetulus) and one African colobine (Colobus guereza). Monkeys were housed at five different captive institutes: Panxi Wildlife Rescue Center (Guizhou, China), Beijing Zoo, Beijing Zoo Breeding Center, Singapore Zoo, and Singapore Zoo Primate Conservation Breeding Center. Captive diets varied widely between institutions, but within an institution, all colobine monkey species were fed nearly identical or identical diets. In addition, four monkey species were present at multiple captive institutes. This allowed us to parse the effects of diet and phylogeny in these captive colobines. Gut microbial communities clustered weakly by host species and strongly by diet, and overall, colobine phylogenetic relationships were not reflected in gut microbiota analyses. Core microbiota analyses also identified several key taxa-including microbes within the Ruminococcaceae and Lachnospiraceae families-that were shared by over 90% of the monkeys in this study. Microbial species within these families include many butyrate producers that are important for GI health. These results highlight the importance of diet in captive colobines.

Face Processing Systems: From Neurons to Real-World Social Perception

Primate face processing depends on a distributed network of interlinked face-selective areas composed of face-selective neurons. In both humans and macaques, the network is divided into a ventral stream and a dorsal stream, and the functional similarities of the areas in humans and macaques indicate they are homologous. Neural correlates for face detection, holistic processing, face space, and other key properties of human face processing have been identified at the single neuron level, and studies providing causal evidence have established firmly that face-selective brain areas are central to face processing. These mechanisms give rise to our highly accurate familiar face recognition but also to our error-prone performance with unfamiliar faces. This limitation of the face system has important implications for consequential situations such as eyewitness identification and policing.

The Effect of Prenatal Alcohol Exposure on Fetal Growth and Cardiovascular Parameters in a Baboon Model of Pregnancy

Prenatal alcohol exposure often results in an array of fetal developmental abnormalities termed fetal alcohol spectrum disorders (FASDs). Despite the high prevalence of FASDs, the pathophysiology of fetal damage by alcohol remains poorly understood. One of the major obstacles in studying fetal development in response to alcohol exposure is the inability to standardize the amount, pattern of alcohol consumption, and peak blood alcohol levels in pregnant mothers. In the present study, we used Doppler ultrasonography to assess fetal growth and cardiovascular parameters in response to alcohol exposure in pregnant baboons. Baboons were subjected to gastric alcohol infusion 3 times during the second trimester equivalent to human pregnancy, with maternal blood alcohol levels reaching 80 mg/dL within 30 to 60 minutes following alcohol infusion. The control group received a drink that was isocaloric to the alcohol-containing one. Doppler ultrasonography was used for longitudinal assessment of fetal biometric parameters and fetal cardiovascular indices. Fetal abdominal and head circumferences, but not femur length, were significantly decreased in alcohol-exposed fetuses near term. Peak systolic velocity of anterior and middle cerebral arteries decreased during episodes of alcohol intoxication, but there was no difference in Doppler indices between groups near term. Acute alcohol intoxication affected fetal cerebral blood flow independent of changes in the fetal cardiac output. Unlike fetal growth parameters, changes in vascular indices did not persist over gestation. In summary, alcohol effects on fetal growth and on fetal vascular function have different time courses.

Speciation over the edge: gene flow among non-human primate species across a formidable biogeographic barrier

Many genera of terrestrial vertebrates diversified exclusively on one or the other side of Wallace's Line, which lies between Borneo and Sulawesi islands in Southeast Asia, and demarcates one of the sharpest biogeographic transition zones in the world. Macaque monkeys are unusual among vertebrate genera in that they are distributed on both sides of Wallace's Line, raising the question of whether dispersal across this barrier was an evolutionary one-off or a more protracted exchange-and if the latter, what were the genomic consequences. To explore the nature of speciation over the edge of this biogeographic divide, we used genomic data to test for evidence of gene flow between macaque species across Wallace's Line after macaques colonized Sulawesi. We recovered evidence of post-colonization gene flow, most prominently on the X chromosome. These results are consistent with the proposal that gene flow is a pervasive component of speciation-even when barriers to gene flow seem almost insurmountable.

Paleobiogeography: Documenting the Ebb and Flow of Evolutionary Diversification

Historical biogeography has recently experienced a significant advancement in three integrated areas. The first is the adoption of an ontology of complexity, replacing the traditional ontology of simplicity, or a priori parsimony; simple and elegant models of the biosphere are not sufficient for explaining the geographical context of the origin of species and their post-speciation movements, producing evolutionary radiations and complex multi-species biotas. The second is the development of a powerful method for producing area cladograms from complex data, especially cases of reticulated area relationships, without loss of information. That method, called Phylogenetic Analysis for Comparing trees (PACT), is described herein. The third element is the replacement of the model of maximum vicariance with the model called the Taxon Pulse hypothesis. PACT analysis of Hominoidea, Hyaenidae, and Proboscidea beginning in the Miocene, reveals that all three groups share a general episode of species formation in Africa in the early Miocene, followed by “out of Africa” expansion into Europe, Asia and North America, a second general episode of species formation in Asia in the mid-Miocene, followed by “out of Asia” expansion into Africa, Europe and North America. Finally, there were two additional “out of Africa” events during the late Miocene and into the Pliocene, the last one setting the stage for the emergence and spread ofHomo. In addition to these shared episodes of vicariance and dispersal, each group exhibits clade-specific within-area and peripheral isolates speciation events. The complex history of dispersal and speciation over largeareas exhibited by hominoids is part of a more general historyof biotic diversification by taxon pulses.

Experimental transfusion-induced Babesia microti infection: dynamics of parasitemia and immune responses in a rhesus macaque model

BACKGROUND

Babesiosis is an emerging tick-borne infection in humans. The increasing numbers of reported cases of transfusion-associated babesiosis (TAB), primarily caused by Babesia microti, represents a concern for the safety of the US blood supply.

STUDY DESIGN AND METHODS

This study investigated kinetics of parasitemia and innate immune responses and dynamics of antibody responses during B. microti infection in rhesus macaques (RMs) using blood smears, quantitative polymerase chain reaction (qPCR), flow cytometry, and indirect fluorescent antibody testing. A total of six monkeys were transfused with either hamster or monkey-passaged B. microti-infected red blood cells (two and four monkeys, respectively) simulating TAB.

RESULTS

The prepatent period in monkeys inoculated with hamster-passaged B. microti was 35 days compared with 4 days in monkeys transfused with monkey-passaged B. microti; the latter monkeys also had markedly higher parasitemia levels. The duration of the window period from the first detected parasitemia by qPCR analysis to the first detected antibody response ranged from 10 to 17 days. Antibody responses fluctuated during the course of the infection. Innate responses assessed by the frequencies of monocytes and activated B cells correlated with the kinetics and magnitude of parasitemia. On Day 14, additional activation peaks were noted for CD14+CD16+ and CD14-CD16+ monocytes and for CD11c+ myeloid dendritic cells, but only in animals transfused with monkey-passaged B. microti. Parasitemia persisted in these immunocompetent animals, similar to human infection.

CONCLUSION

The results suggest that transfusion-associated transmission of B. microti leads to rapid onset of parasitemia (Day 4) in RMs, detectable antibody response 14 days later, and persistent parasitemia.

Functional evolution of new and expanded attention networks in humans

Macaques are often used as a model system for invasive investigations of the neural substrates of cognition. However, 25 million years of evolution separate humans and macaques from their last common ancestor, and this has likely substantially impacted the function of the cortical networks underlying cognitive processes, such as attention. We examined the homology of frontoparietal networks underlying attention by comparing functional MRI data from macaques and humans performing the same visual search task. Although there are broad similarities, we found fundamental differences between the species. First, humans have more dorsal attention network areas than macaques, indicating that in the course of evolution the human attention system has expanded compared with macaques. Second, potentially homologous areas in the dorsal attention network have markedly different biases toward representing the contralateral hemifield, indicating that the underlying neural architecture of these areas may differ in the most basic of properties, such as receptive field distribution. Third, despite clear evidence of the temporoparietal junction node of the ventral attention network in humans as elicited by this visual search task, we did not find functional evidence of a temporoparietal junction in macaques. None of these differences were the result of differences in training, experimental power, or anatomical variability between the two species. The results of this study indicate that macaque data should be applied to human models of cognition cautiously, and demonstrate how evolution may shape cortical networks.

Does target animacy influence manual laterality of monkeys? First answer from northern pig-tailed macaques (Macaca leonina)

The evolutionary origin of human right-handedness remains unclear. Many factors such as emotion and tool use have been implicated in primate handedness evolution. With regard to emotional lateralization, most related research focuses on facial asymmetry and behavioral laterality under the non-social context, whereas few studies investigate social laterality. This study, for the first time, investigates the effect of target animacy on hand preference in Old World monkeys, compares our findings with previous related studies in great apes and humans, and aids in filling the knowledge gap on primate handedness evolution. Nine captive northern pig-tailed macaques (Macaca leonina) were chosen as focal subjects in this study. There was no group-level handedness for both animate and inanimate targets. No significant interaction was found between lateral hand use and target animacy. Left-hand use was more frequent than right-hand use for animate targets, whereas right-hand use was more frequent than left-hand use for inanimate targets, both of which demonstrate no significant level. On the whole, northern pig-tailed macaques showed a similar tendency as that in great apes and humans. Regarding handedness linked with emotive stimuli, it is likely that Old World monkeys, great apes and humans evolved from a common ancestor.

Molecular evolution of the CYP2D subfamily in primates: purifying selection on substrate recognition sites without the frequent or long-tract gene conversion

The human cytochrome P450 (CYP) 2D6 gene is a member of the CYP2D gene subfamily, along with the CYP2D7P and CYP2D8P pseudogenes. Although the CYP2D6 enzyme has been studied extensively because of its clinical importance, the evolution of the CYP2D subfamily has not yet been fully understood. Therefore, the goal of this study was to reveal the evolutionary process of the human drug metabolic system. Here, we investigate molecular evolution of the CYP2D subfamily in primates by comparing 14 CYP2D sequences from humans to New World monkey genomes. Window analysis and statistical tests revealed that entire genomic sequences of paralogous genes were extensively homogenized by gene conversion during molecular evolution of CYP2D genes in primates. A neighbor-joining tree based on genomic sequences at the nonsubstrate recognition sites showed that CYP2D6 and CYP2D8 genes were clustered together due to gene conversion. In contrast, a phylogenetic tree using amino acid sequences at substrate recognition sites did not cluster the CYP2D6 and CYP2D8 genes, suggesting that the functional constraint on substrate specificity is one of the causes for purifying selection at the substrate recognition sites. Our results suggest that the CYP2D gene subfamily in primates has evolved to maintain the regioselectivity for a substrate hydroxylation activity between individual enzymes, even though extensive gene conversion has occurred across CYP2D coding sequences.

Mitogenomics of the Old World monkey tribe Papionini

Background

The evolutionary history of the Old World monkey tribe Papionini comprising the genera Macaca, Mandrillus, Cercocebus, Lophocebus, Theropithecus, Rungwecebus and Papio is still matter of debate. Although the African Papionini (subtribe Papionina) are generally considered to be the sister lineage to the Asian Papionini (subtribe Macacina), previous studies based on morphological data, nuclear or mitochondrial sequences have shown contradictory phylogenetic relationships among and within both subtribes. To further elucidate the phylogenetic relationships among papionins and to estimate divergence ages we generated mitochondrial genome data and combined them with previously published sequences.

Results

Our mitochondrial gene tree comprises 33 papionins representing all genera of the tribe except Rungwecebus. In contrast to most previous studies, the obtained phylogeny suggests a division of the Papionini into three main mitochondrial clades with similar ages: 1) Papio, Theropithecus, Lophocebus; 2) Mandrillus, Cercocebus; and 3) Macaca; the Mandrillus + Cercocebus clade appears to be more closely related to Macaca than to the other African Papionini. Further, we find paraphyletic relationships within the Mandrillus + Cercocebus clade as well as in Papio. Relationships among Theropithecus, Lophocebus and Papio remain unresolved. Divergence ages reveal initial splits within the three mitochondrial clades around the Miocene/Pliocene boundary and differentiation of Macaca species groups occurred on a similar time scale as those found between genera of the subtribe Papionina.

Conclusion

Due to the largely well-resolved mitochondrial phylogeny, our study provides new insights into the evolutionary history of the Papionini. Results show some contradictory relationships in comparison to previous analyses, notably the paraphyly within the Cercocebus + Mandrillus clade and three instead of only two major mitochondrial clades. Divergence ages among species groups of macaques are similar to those among African Papionini genera, suggesting that diversification of the mitochondrial genome is of a similar magnitude in both subtribes. However, since our mitochondrial tree represents just a single gene tree that most likely does not reflect the true species tree, extensive nuclear sequence data is required to illuminate the true species phylogeny of papionins and to trace possible ancient hybridization events among lineages.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-014-0176-1) contains supplementary material, which is available to authorized users.

The tempo and mode of New World monkey evolution and biogeography in the context of phylogenomic analysis

The development and evolution of organisms is heavily influenced by their environment. Thus, understanding the historical biogeography of taxa can provide insights into their evolutionary history, adaptations and trade-offs realized throughout time. In the present study we have taken a phylogenomic approach to infer New World monkey phylogeny, upon which we have reconstructed the biogeographic history of extant platyrrhines. In order to generate sufficient phylogenetic signal within the New World monkey clade, we carried out a large-scale phylogenetic analysis of approximately 40 kb of non-genic genomic DNA sequence in a 36 species subset of extant New World monkeys. Maximum parsimony, maximum likelihood and Bayesian inference analysis all converged on a single optimal tree topology. Divergence dating and biogeographic analysis reconstruct the timing and geographic location of divergence events. The ancestral area reconstruction describes the geographic locations of the last common ancestor of extant platyrrhines and provides insight into key biogeographic events occurring during platyrrhine diversification. Through these analyses we conclude that the diversification of the platyrrhines took place concurrently with the establishment and diversification of the Amazon rainforest. This suggests that an expanding rainforest environment rather than geographic isolation drove platyrrhine diversification.

Phylogeny and historical biogeography of Isodon (Lamiaceae): rapid radiation in south-west China and Miocene overland dispersal into Africa

Rapid organismal radiations occurring on the Qinghai-Tibetan Plateau (QTP) and the mechanisms underlying Asia-Africa intercontinental disjunctions have both attracted much attention from evolutionary biologists. Here we use the genus Isodon (Lamiaceae), a primarily East Asian lineage with disjunct species in central and southern Africa, as a case study to shed light upon these processes. The molecular phylogeny and biogeographic history of Isodon were reconstructed using sequences of three plastid markers, the nuclear ribosomal internal transcribed spacer (nrITS), and a low-copy nuclear gene (LEAFY intron II). The evolution of chromosome numbers in this genus was also investigated using probabilistic models. Our results support a monophyletic Isodon that includes the two disjunct African species, both of which likely formed through allopolyploidy. An overland migration from Asia to Africa through Arabia during the early Miocene is proposed as the most likely explanation for the present disjunct distribution of Isodon. The opening of the Red Sea in the middle Miocene may appear to have had a major role in disrupting floristic exchange between Asia and Africa. In addition, a rapid radiation of Isodon was suggested to occur in the late Miocene. It corresponds with one of the major uplifts of the QTP and subsequent aridification events. Our results support the hypothesis that geological and climatic events play important roles in driving biological diversification of organisms distributed in the QTP area.

The effective population sizes of the anthropoid ancestors of the human-chimpanzee lineage provide insights on the historical biogeography of the great apes

The recent development of methods that apply coalescent theory to phylogenetic problems has enabled the study of the population-level phenomena that drove the diversification of anthropoid primates. Effective population size, Ne, is one of the main parameters that constitute the theoretical underpinning of these new analytical approaches. For this reason, the ancestral N(e) of selected primate lineages has been thoroughly investigated. However, for some of these lineages, the estimates of ancestral N(e) reported in several studies present significant variation. This is the case for the common ancestor of humans and chimpanzees. Moreover, several ancestral anthropoid lineages have been ignored in the studies conducted so far. Because N(e) is fundamental to understand historic species demography, it is a crucial component of a complete description of the historical scenario of primate evolution. It also provides information that is helpful for differentiating between competing biogeographical hypotheses. In this study, the effective population sizes of the anthropoid ancestors of the human-chimp lineage are inferred using data sets of coding and noncoding sequences. A general pattern of a serial decline of population sizes is found between the ancestral lineage of Anthropoidea and that of Homo and Pan. When the theoretical distribution of gene trees was derived from the parametric estimates obtained, it closely corresponded to the empirical frequency of inferred gene trees along the genome. The most abrupt decrease of N(e) was found between the ancestors of all great apes and those of the African great apes alone. This suggests the occurrence of a genetic bottleneck during the evolution of Homininae, which corroborates the origin of African apes from a Eurasian ancestor.

Continuities in emotion lateralization in human and non-human primates

Where hemispheric lateralization was once considered an exclusively human trait, it is increasingly recognized that hemispheric asymmetries are evident throughout the animal kingdom. Emotion is a prime example of a lateralized function: given its vital role in promoting adaptive behavior and hence survival, a growing body of research in affective neuroscience is working to illuminate the cortical bases of emotion processing. Presuming that human and non-human primates evolved from a shared ancestor, one would anticipate evidence of organizational continuity in the neural substrate supporting emotion processing. This paper thus reviews research examining the patterns of lateralization for the expression and perception of facial emotion in non-human primates, aiming to determine whether the patterns of hemispheric asymmetry that characterize the human brain are similarly evident in other primate species. As such, this review seeks to enhance understanding of the evolution of hemispheric specialization for emotion, using emotion lateralization in non-human primates as a window through which to view emotion lateralization in humans.

Face recognition systems in monkey and human: are they the same thing?

Primate societies are based on face recognition. Face recognition mechanisms have been studied most extensively in humans and macaque monkeys. In both species, multiple brain areas specialized for face processing have been found, and their functional properties are characterized with increasing detail, so we can now begin to address questions about similarities and differences of face-recognition systems across species with 25 million years of separate evolution. Both systems are organized into multiple face-selective cortical areas in spatial arrangements and with functional specializations, implying both hierarchical and parallel modes of information processing. Yet open questions about homologies remain. To address these, future studies employing similar techniques and experimental designs across multiple species are needed to identify a putative core primate face processing system and to understand its differentiations into the multiple branches of the primate order.

Face recognition systems in monkey and human: are they the same thing?

Primate societies are based on face recognition. Face recognition mechanisms have been studied most extensively in humans and macaque monkeys. In both species, multiple brain areas specialized for face processing have been found, and their functional properties are characterized with increasing detail, so we can now begin to address questions about similarities and differences of face-recognition systems across species with 25 million years of separate evolution. Both systems are organized into multiple face-selective cortical areas in spatial arrangements and with functional specializations, implying both hierarchical and parallel modes of information processing. Yet open questions about homologies remain. To address these, future studies employing similar techniques and experimental designs across multiple species are needed to identify a putative core primate face processing system and to understand its differentiations into the multiple branches of the primate order.

When the single matters more than the group: very high false positive rates in single case Voxel Based Morphometry

Voxel Based Morphometry (VBM) studies typically involve a comparison between groups of individuals; this approach however does not allow inferences to be made at the level of the individual. In recent years, an increasing number of research groups have attempted to overcome this issue by performing single case studies, which involve the comparison between a single subject and a control group. However, the interpretation of the results is problematic; for instance, any significant difference might be driven by individual variability in neuroanatomy rather than the neuropathology of the disease under investigation, or might represent a false positive due to the data being sampled from non-normally distributed populations. The aim of the present investigation was to empirically estimate the likelihood of detecting significant differences in gray matter volume in individuals free from neurological or psychiatric diagnosis. We compared a total of 200 single subjects against a group of 16 controls matched for age and gender, using two independent datasets from the Neuroimaging Informatics Tools and Resources Clearinghouse. We report that the chance of detecting a significant difference in a disease-free individual is much higher than previously expected; for instance, using a standard voxel-wise threshold of p<0.05 (corrected) and an extent threshold of 10 voxels, the likelihood of a single subject showing at least one significant difference is as high as 93.5% for increases and 71% for decreases. We also report that the chance of detecting significant differences was greatest in frontal and temporal cortices and lowest in subcortical regions. The chance of detecting significant differences was inversely related to the degree of smoothing applied to the data, and was higher for unmodulated than modulated data. These results were replicated in the two independent datasets. By providing an empirical estimation of the number of significant increases and decreases to be expected in each cortical and subcortical region in disease-free individuals, the present investigation could inform the interpretation of future single case VBM studies.

Characterization of the major histocompatibility complex class I A alleles in cynomolgus macaques of Vietnamese origin

Cynomolgus macaques (Macaca fascicularis, Mafa) have emerged as an important animal model for infectious disease and transplantation research. Extensive characterization of their major histocompatibility complex (MHC) polymorphism regions therefore becomes urgently required. In this study, we identified 41 MHC class I A nucleotide sequences in 34 unrelated cynomolgus macaques of Vietnamese origin farmed in Southern China, including eight novel Mafa-A sequences. We found two sequences with perfect identity and six sequences with close similarity to previously defined MHC class I alleles from other populations, especially from Indonesian-origin macaques. We also found three Vietnamese-origin cynomolgus macaque MHC class I sequences for which the predicted protein sequences identical throughout their B and F binding pockets to Mamu-A1*001:01 and Mamu-A3*13:03, respectively. This is important because Mamu-A1*001:01 and Mamu-A3*13:03 are associated with longer survival and lower set-point viral load in simian immunodeficiency virus (SIV)-infected rhesus monkeys. These findings have implications for the evolutionary history of Vietnamese-origin cynomolgus macaque as well as for the use of this model in SIV/SHIV (a virus combining parts of the HIV and SIV genomes) research.

Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix

Phylogenetic relationships, divergence times, and patterns of biogeographic descent among primate species are both complex and contentious. Here, we generate a robust molecular phylogeny for 70 primate genera and 367 primate species based on a concatenation of 69 nuclear gene segments and ten mitochondrial gene sequences, most of which were extracted from GenBank. Relaxed clock analyses of divergence times with 14 fossil-calibrated nodes suggest that living Primates last shared a common ancestor 71-63 Ma, and that divergences within both Strepsirrhini and Haplorhini are entirely post-Cretaceous. These results are consistent with the hypothesis that the Cretaceous-Paleogene mass extinction of non-avian dinosaurs played an important role in the diversification of placental mammals. Previous queries into primate historical biogeography have suggested Africa, Asia, Europe, or North America as the ancestral area of crown primates, but were based on methods that were coopted from phylogeny reconstruction. By contrast, we analyzed our molecular phylogeny with two methods that were developed explicitly for ancestral area reconstruction, and find support for the hypothesis that the most recent common ancestor of living Primates resided in Asia. Analyses of primate macroevolutionary dynamics provide support for a diversification rate increase in the late Miocene, possibly in response to elevated global mean temperatures, and are consistent with the fossil record. By contrast, diversification analyses failed to detect evidence for rate-shift changes near the Eocene-Oligocene boundary even though the fossil record provides clear evidence for a major turnover event ("Grande Coupure") at this time. Our results highlight the power and limitations of inferring diversification dynamics from molecular phylogenies, as well as the sensitivity of diversification analyses to different species concepts.