New World Monkeys Research Articles

Bocaparvovirus,ErythroparvovirusandTetraparvovirusin New World Primates from Central America

Parvoviruses in the genera Bocaparvovirus (HBoV), Erythroparvovirus (B19) and Tetraparvovirus (PARV4) are the only autonomous parvoviruses known to be associated with human and non-human primates based on studies and clinical cases in humans worldwide and non-human primates in Asia and Africa. Here, the presence of these agents with pathogenic potential was assessed by PCR in blood and faeces from 55 howler monkeys, 112 white-face monkeys, 3 squirrel monkeys and 127 spider monkeys in Costa Rica and El Salvador. Overall, 3.7% (11/297) of the monkeys had HboV DNA, 0.67% (2/297) had B19 DNA, and 14.1% (42/297) had PARV4 DNA, representing the first detection of these viruses in New World Primates (NWP). Sex was significantly associated with the presence of HBoV, males having greater risk up to nine times compared with females. Captivity was associated with increased prevalence for PARV4 and when all viruses were analysed together. This study provides compelling molecular evidence of parvoviruses in NWPs and underscores the importance of future research aimed at understanding how these viruses behave in natural environments of the Neotropics and what variables may favour their presence and transmission.

The Early to late Middle Miocene mammalian assemblages from the Cura-Mallín Formation, at Lonquimay, southern Central Andes, Chile (~38°S): Biogeographical and paleoenvironmental implications

The Cura-Mallín Formation consists of a series of upper Oligocene to Upper Miocene volcanic and sedimentary rocks deposited in continental settings that crop out in the Andean Cordillera in Chile and Argentina between ~37° and 39°S. Since the 1990s few fossil mammals have been recovered from this unit in the surroundings of Lonquimay, south-central Chile (38.5°S), and all of them were assigned to the Early Miocene. After a reassessment of the taxonomic affinities of the fauna so far recovered from the Cura-Mallín Formation in the Lonquimay area, and based on the radioisotopic ages of the fossil-bearing localities, here we recognized two chronological distinctive mammalian assemblages: one of Early Miocene age (probably Colhuehuapian–Santacrucian SALMA), which includes Nesodon imbricatus and Parastrapotherium sp.; and a second one of late Middle Miocene age (12.8–11.6 Ma; Serravallian; Mayoan SALMA), which includes glyptodonts (Glyptodontidae indeterminate), armadillos (Eutatini indeterminate), macraucheniids (Theosodon sp.), a new interatheriid species (Protypotherium concepcionensis sp. nov.), and a likely platyrrhine monkey. Therefore, in contrast with previous interpretations, the fauna from Lonquimay is not uniquely restricted to the Early Miocene. The fossil mammals and plants recognized from the area indicate the persistence of mostly temperate and forested habitats with permanent bodies of water during the Early to latest Middle Miocene. This suggests that this part of the Andean Cordillera (38°‒39°S) did not reach enough paleoaltitudes (>1000 m) to cause an important orographic rain shadow effect in the foreland basins at least after the late Middle Miocene (c. 12 Ma). However, the role of Neogene South Hemisphere climatic changes in triggering, or reinforcing, the foreland desertification along the south-central Andes is an additional factor that cannot be discarded.

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage.

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.

Cyto- and Myelo-Architecture of the Amygdaloid Complex of the Common Marmoset Monkey (Callithrix jacchus).

The amygdaloid complex (AC) is a heterogeneous aggregate of nuclei located in the rostromedial region of the temporal lobe. In addition to being partly connected among themselves, the AC nuclei are strongly interconnected with the cerebral cortex, striatum, basal forebrain, hypothalamus and brainstem. Animal and human functional studies have established that the AC is a central hub of the neuronal networks supporting emotional responsivity, particularly its negative/aversive components. Dysfunction of AC circuits in humans has been implicated in anxiety, depression, schizophrenia and bipolar disorder. The small New-World marmoset monkey (Callithrix jacchus) has recently become a key model for neuroscience research. However, the nuclear and fiber tract organization of marmoset AC has not been examined in detail. Thus, the extent to which it can be compared to the AC of Old-World (human and macaque) primates is yet unclear. Here, using Nissl and acetylcholinesterase (AChE) histochemical stains as a reference, we analyzed the cytoarchitecture and nuclear parcellation of the marmoset AC. In addition, given the increasing relevance of tractographic localization for high-resolution in vivo imaging studies in non-human primates, we also identified the myelin fiber tracts present within and around the AC as revealed by the Gallyas method. The present study provides a detailed atlas of marmoset AC. Moreover, it reveals that, despite phylogenetic distance and brain size differences, every nucleus and myelinated axon bundle described in human and macaque studies can be confidently recognized in marmosets.

Amplification Dynamics of Platy-1 Retrotransposons in the Cebidae Platyrrhine Lineage.

Platy-1 elements are Platyrrhine-specific, short interspersed elements originally discovered in the Callithrix jacchus (common marmoset) genome. To date, only the marmoset genome has been analyzed for Platy-1 repeat content. Here, we report full-length Platy-1 insertions in other New World monkey (NWM) genomes (Saimiri boliviensis, squirrel monkey; Cebus imitator, capuchin monkey; and Aotus nancymaae, owl monkey) and analyze the amplification dynamics of lineage-specific Platy-1 insertions. A relatively small number of full-length and lineage-specific Platy-1 elements were found in the squirrel, capuchin, and owl monkey genomes compared with the marmoset genome. In addition, only a few older Platy-1 subfamilies were recovered in this study, with no Platy-1 subfamilies younger than Platy-1-6. By contrast, 62 Platy-1 subfamilies were discovered in the marmoset genome. All of the lineage-specific insertions found in the squirrel and capuchin monkeys were fixed present. However, ∼15% of the lineage-specific Platy-1 loci in Aotus were polymorphic for insertion presence/absence. In addition, two new Platy-1 subfamilies were identified in the owl monkey genome with low nucleotide divergences compared with their respective consensus sequences, suggesting minimal ongoing retrotransposition in the Aotus genus and no current activity in the Saimiri, Cebus, and Sapajus genera. These comparative analyses highlight the finding that the high number of Platy-1 elements discovered in the marmoset genome is an exception among NWM analyzed thus far, rather than the rule. Future studies are needed to expand upon our knowledge of Platy-1 amplification in other NWM genomes.

Expression of Transcripts in Marmoset Oocytes Retrieved during Follicle Isolation Without Gonadotropin Induction.

The in vitro maturation of oocytes is frequently used as an assisted reproductive technique (ART), and has been successfully established in humans and rodents. To overcome the limitations of ART, novel procedures for the in vitro maturation of early follicles are emerging. During the follicle isolation procedure, the unintended rupture of each follicle leads to a release of extra oocytes. Such oocytes, which are obtained during follicle isolation from marmosets, can be used for early maturation studies. Marmoset (Callithrix jacchus), which is classified as a new-world monkey, is a novel model that has been employed in reproductive biomedical research, as its reproductive physiology is similar to that of humans in several aspects. The ovaries of female marmosets were collected, and the excess oocytes present during follicle isolation were retrieved without pre-gonadotropin induction. Each oocyte was matured in vitro for 48 h in the presence of various concentrations of human chorionic gonadotropin (hCG) and epidermal growth factor (EGF), and the maturity of oocytes and optimal maturation conditions were evaluated. Each oocyte was individually reverse-transcribed, and the expression of mRNAs and microRNAs (miRs) were analyzed. Concentrations of hCG significantly affected the maturation rate of oocytes [the number of metaphase II (MII) oocytes]. The expression of BMP15 and ZP1 was highest when the oocytes were matured using 100 IU/L of hCG without pre-treatment with gonadotropins, and that of Cja-mir-27a was highest when cultured with follicle stimulating hormone. These results suggest that these up-regulated miRs affect the maturation of oocytes. Interactions with other protein networks were analyzed, and a strong association of BMP15 and ZP1 with sperm binding receptor (ACR), anti-Müllerian hormone (AMH), and AMH receptor was demonstrated, which is related to the proliferation of granulosa cells. Collectively, on the basis of these results, the authors propose optimal maturation conditions of excess oocytes of marmoset without in vivo gonadotropin treatment, and demonstrated the roles of miRs in early oocyte maturation at the single-cell level in marmosets.

Oxytocin structure and function in New World monkeys: from pharmacology to behavior.

Oxytocin (OT) is a hypothalamic nonapeptide that mediates a host of physiological and behavioral processes including reproductive physiology and social attachments. While the OT sequence structure is highly conserved among mammals, New World monkeys (NWMs) represent an unusual "hot spot" in OT structure variability among mammals. At least 6 distinct OT ligand variants among NWMs exist, yet it is currently unclear whether these evolved structural changes result in meaningful functional consequences. NWMs offer a new area to explore how these modifications to OT and its canonical G-protein coupled OT receptor (OTR) may mediate specific cellular, physiological and behavioral outcomes. In this review, we highlight relationships between OT ligand and OTR structural variability, specifically examining coevolution between OT ligands, OTRs, and physiological and behavioral phenotypes across NWMs. We consider whether these evolved modifications to the OT structure alter pharmacological profiles at human and marmoset OTRs, including changes to receptor binding, intracellular signaling and receptor internalization. Finally, we evaluate whether exogenous manipulation using OT variants in marmoset monkeys differentially enhance or impair behavioral processes involved in social relationships between pairmates, opposite-sex strangers, and parents and their offspring. Overall, it appears that changes to OT ligands in NWMs result in important changes ranging from cellular signaling to broad measures of social behavior.

Adenoviruses of the most ancient primate lineages support the theory on virus-host co-evolution.

The scarcity or complete lack of information on the adenoviruses (AdVs) occurring in the most ancient non-human primates resulted in the initiation of a study for exploring their abundance and diversity in prosimians and New World monkeys (NWMs). In order to assess the variability of these AdVs and the possible signs of the hypothesised virus-host co-evolution, samples from almost every family of NWMs and prosimians were screened for the presence of AdVs. A PCRscreening of 171 faecal or organ samples from live or dead, captive or wild-living prosimians and NWMs was performed. The PCR products from the gene of the IVa2 protein were sequenced and used in phylogeny calculations. The presence of 10 and 15 new AdVs in seven and ten different species of prosimians and NWMs was revealed, respectively. Phylogenetic analysis indicated that the tentative novel AdVs cluster into two separate groups, which form the most basal branches among the primate AdVs, and therefore support the theory on the co-evolution of primate AdVs with their hosts. This is the first report that provides a comprehensive overview of the AdVs occurring in prosimians and NWMs, and the first insight into the evolutionary relationships among AdVs from all major primate groups.

DNA Polymerase Sequences of New World Monkey Cytomegaloviruses: Another Molecular Marker with Which To Infer Platyrrhini Systematics.

Over the past few decades, a large number of studies have identified herpesvirus sequences from many mammalian species around the world. Among the different nonhuman primate species tested so far for cytomegaloviruses (CMVs), only a few were from the New World. Seeking to identify CMV homologues in New World monkeys (NWMs), we carried out molecular screening of 244 blood DNA samples from 20 NWM species from Central and South America. Our aim was to reach a better understanding of their evolutionary processes within the Platyrrhini parvorder. Using PCR amplification with degenerate consensus primers targeting highly conserved amino acid motifs encoded by the herpesvirus DNA polymerase gene, we characterized novel viral sequences from 12 species belonging to seven genera representative of the three NWM families. BLAST searches, pairwise nucleotide and amino acid sequence comparisons, and phylogenetic analyses confirmed that they all belonged to the Cytomegalovirus genus. Previously determined host taxa allowed us to demonstrate a good correlation between the distinct monophyletic clades of viruses and those of the infected primates at the genus level. In addition, the evolutionary branching points that separate NWM CMVs were congruent with the divergence dates of their hosts at the genus level. These results significantly expand our knowledge of the host range of this viral genus and strongly support the occurrence of cospeciation between these viruses and their hosts. In this respect, we propose that NWM CMV DNA polymerase gene sequences may serve as reliable molecular markers with which to infer Platyrrhini phylogenetics.IMPORTANCE Investigating evolutionary processes between viruses and nonhuman primates has led to the discovery of a large number of herpesviruses. No study published so far on primate cytomegaloviruses has extensively studied New World monkeys (NWMs) at the subspecies, species, genus, and family levels. The present study sought to identify cytomegalovirus homologues in NWMs and to decipher their evolutionary relationships. This led us to characterize novel viruses from 12 of the 20 primate species tested, which are representative of the three NWM families. The identification of distinct viruses in these primates not only significantly expands our knowledge of the host range of this viral genus but also sheds light on its evolutionary history. Phylogenetic analyses and molecular dating of the sequences obtained support a virus-host coevolution.

Binding Characteristics of Two Oxytocin Variants and Vasopressin at Oxytocin Receptors from Four Primate Species with Different Social Behavior Patterns.

A clade of New World monkeys (NWMs) exhibits considerable diversity in both oxytocin (OT) ligand and oxytocin receptor (OTR) structure. Most notable is the variant Pro8-OT, with proline instead of leucine at the eighth position, resulting in a rigid bend in the peptide backbone. A higher proportion of species that express Pro8-OT also engage in biparental care and social monogamy. When marmosets (genus Callithrix), a biparental and monogamous Pro8-OT NWM species, are administered the ancestral Leu8-OT, there is no change in social behavior compared with saline treatment. However, when Pro8-OT is administered, marmosets' sociosexual and prosocial behaviors are altered. The studies here tested the hypothesis that OTR binding affinities and OT-induced intracellular Ca2+ potencies would favor the native OT ligand in OTRs from four primate species, each representing a unique combination of ancestral lineage, breeding system, and native OT ligand: humans (Leu8-OT, monogamous, apes), macaques (Leu8-OT, nonmonogamous, Old World monkey), marmosets (Pro8-OT, monogamous, NWM), and titi monkeys (Leu8-OT, monogamous, NWM). OTRs were expressed in immortalized Chinese hamster ovary cells and tested for intact-cell binding affinities for Pro8-OT, Leu8-OT, and arginine vasopressin (AVP), as well as intracellular Ca2+ signaling after stimulation with Pro8-OT, Leu8-OT, and AVP. Contrary to our hypothesis, Pro8-OT bound at modestly higher affinities and stimulated calcium signaling at modestly higher potencies compared with Leu8-OT in all four primate OTRs. Thus, differences downstream from a ligand-receptor binding event are more likely to explain the different behavioral responses to these two ligands.

Early Arrival and Climatically-Linked Geographic Expansion of New World Monkeys from Tiny African Ancestors.

New World Monkeys (NWM) (platyrrhines) are one of the most diverse groups of primates, occupying today a wide range of ecosystems in the American tropics and exhibiting large variations in ecology, morphology, and behavior. Although the relationships among the almost 200 living species are relatively well understood, we lack robust estimates of the timing of origin, ancestral morphology, and geographic range evolution of the clade. Herein, we integrate paleontological and molecular evidence to assess the evolutionary dynamics of extinct and extant platyrrhines. We develop novel analytical frameworks to infer the evolution of body mass, changes in latitudinal ranges through time, and species diversification rates using a phylogenetic tree of living and fossil taxa. Our results show that platyrrhines originated 5–10 million years earlier than previously assumed, dating back to the Middle Eocene. The estimated ancestral platyrrhine was small—weighing 0.4 kg—and matched the size of their presumed African ancestors. As the three platyrrhine families diverged, we recover a rapid change in body mass range. During the Miocene Climatic Optimum, fossil diversity peaked and platyrrhines reached their widest latitudinal range, expanding as far South as Patagonia, favored by warm and humid climate and the lower elevation of the Andes. Finally, global cooling and aridification after the middle Miocene triggered a geographic contraction of NWM and increased their extinction rates. These results unveil the full evolutionary trajectory of an iconic and ecologically important radiation of monkeys and showcase the necessity of integrating fossil and molecular data for reliably estimating evolutionary rates and trends.

A Penalized Likelihood Framework for High-Dimensional Phylogenetic Comparative Methods and an Application to New-World Monkeys Brain Evolution.

Working with high-dimensional phylogenetic comparative data sets is challenging because likelihood-based multivariate methods suffer from low statistical performances as the number of traits $p $ approaches the number of species $n $ and because some computational complications occur when $p $ exceeds $n$. Alternative phylogenetic comparative methods have recently been proposed to deal with the large $p $ small $n $ scenario but their use and performances are limited. Herein, we develop a penalized likelihood (PL) framework to deal with high-dimensional comparative data sets. We propose various penalizations and methods for selecting the intensity of the penalties. We apply this general framework to the estimation of parameters (the evolutionary trait covariance matrix and parameters of the evolutionary model) and model comparison for the high-dimensional multivariate Brownian motion (BM), Early-burst (EB), Ornstein-Uhlenbeck (OU), and Pagel's lambda models. We show using simulations that our PL approach dramatically improves the estimation of evolutionary trait covariance matrices and model parameters when $p$ approaches $n$, and allows for their accurate estimation when $p$ equals or exceeds $n$. In addition, we show that PL models can be efficiently compared using generalized information criterion (GIC). We implement these methods, as well as the related estimation of ancestral states and the computation of phylogenetic principal component analysis in the R package RPANDA and mvMORPH. Finally, we illustrate the utility of the new proposed framework by evaluating evolutionary models fit, analyzing integration patterns, and reconstructing evolutionary trajectories for a high-dimensional 3D data set of brain shape in the New World monkeys. We find a clear support for an EB model suggesting an early diversification of brain morphology during the ecological radiation of the clade. PL offers an efficient way to deal with high-dimensional multivariate comparative data.

Contrasting patterns of RUNX2 repeat variations are associated with palate shape in phyllostomid bats and New World primates

Establishing the genetic basis that underlies craniofacial variability in natural populations is one of the main topics of evolutionary and developmental studies. One of the genes associated with mammal craniofacial variability is RUNX2, and in the present study we investigated the association between craniofacial length and width and RUNX2 across New World bats (Phyllostomidae) and primates (Catarrhini and Platyrrhini). Our results showed contrasting patterns of association between the glutamate/alanine ratios (Q/A ratio) and palate shape in these highly diverse groups. In phyllostomid bats, we found an association between shorter/broader faces and increase of the Q/A ratio. In New World monkeys (NWM) there was a positive correlation of increasing Q/A ratios to more elongated faces. Our findings reinforced the role of the Q/A ratio as a flexible genetic mechanism that would rapidly change the time of skull ossification throughout development. However, we propose a scenario in which the influence of this genetic adjustment system is indirect. The Q/A ratio would not lead to a specific phenotype, but throughout the history of a lineage, would act along with evolutionary constraints, as well as other genes, as a facilitator for adaptive morphological changes.

Binding and Signaling Properties of the Leu8 and Pro8 Isoforms of Oxytocin for Oxytocin Receptors from Four Primate Species

Among New World monkeys (NWM), there is a remarkable correlation between those species exhibiting social monogamy and biparental behavior and their expression of an oxytocin (OT) variant with proline at the eighth position (Pro8OT) instead of the common mammalian OT ligand that has leucine at position 8 (Leu8OT). In light of evidence for OT involvement in normative and dysfunctional social behavior, a better understanding of the impact of ligand variation on OT binding and signaling could provide insights into the pharmacological modulation of sociality. We tested the hypothesis that Leu8OT and Pro8OT would bind differently to the OT receptors (OTRs) from Leu8OT‐versus Pro8OT‐expressing species. OTRs from four primate species were expressed in Chinese hamster ovary cells, each species representing a unique combination of ancestral lineage, breeding system, and native OT ligand: marmoset (Pro8OT, monogamous, NWM), macaque (Leu8OT, nonmonogamous, Old World monkey), Titi monkey (Leu8OT, monogamous, NWM; an exception to the pattern), and human (Leu8OT). Saturation assays of binding of the OTR antagonist radioligand 125I‐OVTA to intact cells on ice yielded Bmax values (fmol per well of a 96‐well plate) of approximately 100 for marmoset, 10 for macaque, 10 for human, and 30 for Titi. KD values in pM were 350 for marmoset, 150 for macaque, 290 for Titi, and 140 for human. Competition binding assays were conducted with Pro8OT, Leu8OT, and the closely related nonapeptide hormone arginine vasopressin (AVP) for OTRs from all of four species. Contrary to our hypothesis, all of the OTRs exhibited higher affinity for Pro8OT than for Leu8OT. IC50 values in nM for Pro8OT, Leu8OT, and AVP, respectively, were 150, 400, and 2900 for marmoset, 40, 70, and 460 for macaque, 190, 960, and 3900 for Titi, and 20, 90, and 520 for human. Preference for Pro8OT versus Leu8OT was about 2‐fold for marmoset and macaque and about 4‐fold for Titi and human. All of the receptors exhibited a similar 4‐ to 7‐fold lower affinity for AVP than for Leu8OT, as expected. Calcium signaling downstream of OTRs was assessed with FlexStation assays. EC50 values in pM for Pro8OT, Leu8OT, and AVP, respectively, were 50, 160, 430 for marmoset, 1340, 2100, and 7800 for macaque, 600, 1000, and 4900 for Titi, and 70,130, and 230 for human. The higher potencies for marmoset and Titi are likely due to the higher OTR expression in those cells. Preference for Pro8OT versus Leu8OT for calcium signaling was less than 2‐fold for all species except marmoset, with a 3.2‐fold preference. The human receptor showed the smallest preference for Leu8OT versus AVP. Together these data show that differences in OTR ligand binding affinities and/or calcium signaling potencies do not provide an obvious explanation for the different behaviors of Pro8OT‐versus Leu8OT‐expressing species. Differential signaling to other downstream responses remains to be investigated.Support or Funding InformationSupported by NIH grant 1‐R01‐HD089147 to JAF, TFM, and MLT.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Evolution of Melanoma Antigen-A11 (MAGEA11) During Primate Phylogeny.

Melanoma antigen-A11 (MAGE-A11) is an X-linked and primate-specific steroid hormone receptor transcriptional coregulator and proto-oncogenic protein whose increased expression promotes the growth of prostate cancer. The MAGEA11 gene is expressed at low levels in normal human testis, ovary, and endometrium, and at highest levels in castration-resistant prostate cancer. Annotated genome predictions throughout the surviving primate lineage show that MAGEA11 acquired three 5' coding exons unique within the MAGEA subfamily during the evolution of New World monkeys (NWM), Old World monkeys (OWM), and apes. MAGE-A11 in all primates has a conserved FXXIF coactivator-binding motif that suggests interaction with p160 coactivators contributed to its early evolution as a transcriptional coregulator. An ancestral form of MAGE-A11 in the more distantly related lemur has significant amino acid sequence identity with human MAGE-A11, but lacks coregulator activity based on the absence of the three 5' coding exons that include a nuclear localization signal (NLS). NWM MAGE-A11 has greater amino acid sequence identity than lemur to human MAGE-A11, but inframe premature stop codons suggest that MAGEA11 is a pseudogene in NWM. MAGE-A11 in OWM and apes has nearly identical 5' coding exon amino acid sequence and conserved interaction sites for p300 acetyltransferase and cyclin A. We conclude that the evolution of MAGEA11 within the lineage leading to OWM and apes resulted in steroid hormone receptor transcriptional coregulator activity through the acquisition of three 5' coding exons that include a NLS sequence and nonsynonymous substitutions required to interact with cell cycle regulatory proteins and transcription factors.

Recently integrated Alu insertions in the squirrel monkey (Saimiri) lineage and application for population analyses

BackgroundThe evolution of Alu elements has been ongoing in primate lineages and Alu insertion polymorphisms are widely used in phylogenetic and population genetics studies. Alu subfamilies in the squirrel monkey (Saimiri), a New World Monkey (NWM), were recently reported. Squirrel monkeys are commonly used in biomedical research and often require species identification. The purpose of this study was two-fold: 1) Perform locus-specific PCR analyses on recently integrated Alu insertions in Saimiri to determine their amplification dynamics, and 2) Identify a subset of Alu insertion polymorphisms with species informative allele frequency distributions between the Saimiri sciureus and Saimiri boliviensis groups.ResultsPCR analyses were performed on a DNA panel of 32 squirrel monkey individuals for 382 Alu insertion events ≤2% diverged from 46 different Alu subfamily consensus sequences, 25 Saimiri specific and 21 NWM specific Alu subfamilies. Of the 382 loci, 110 were polymorphic for presence / absence among squirrel monkey individuals, 35 elements from 14 different Saimiri specific Alu subfamilies and 75 elements from 19 different NWM specific Alu subfamilies (13 of 46 subfamilies analyzed did not contain polymorphic insertions). Of the 110 Alu insertion polymorphisms, 51 had species informative allele frequency distributions between Saimiri sciureus and Saimiri boliviensis groups.ConclusionsThis study confirms the evolution of Alu subfamilies in Saimiri and provides evidence for an ongoing and prolific expansion of these elements in Saimiri with many active subfamilies concurrently propagating. The subset of polymorphic Alu insertions with species informative allele frequency distribution between Saimiri sciureus and Saimiri boliviensis will be instructive for specimen identification and conservation biology.

Human migration and the spread of malaria parasites to the New World

We examined the mitogenomes of a large global collection of human malaria parasites to explore how and when Plasmodium falciparum and P. vivax entered the Americas. We found evidence of a significant contribution of African and South Asian lineages to present-day New World malaria parasites with additional P. vivax lineages appearing to originate from Melanesia that were putatively carried by the Australasian peoples who contributed genes to Native Americans. Importantly, mitochondrial lineages of the P. vivax-like species P. simium are shared by platyrrhine monkeys and humans in the Atlantic Forest ecosystem, but not across the Amazon, which most likely resulted from one or a few recent human-to-monkey transfers. While enslaved Africans were likely the main carriers of P. falciparum mitochondrial lineages into the Americas after the conquest, additional parasites carried by Australasian peoples in pre-Columbian times may have contributed to the extensive diversity of extant local populations of P. vivax.

A digital 3D atlas of the marmoset brain based on multi-modal MRI

The common marmoset (Callithrix jacchus) is a New-World monkey of growing interest in neuroscience. Magnetic resonance imaging (MRI) is an essential tool to unveil the anatomical and functional organization of the marmoset brain. To facilitate identification of regions of interest, it is desirable to register MR images to an atlas of the brain. However, currently available atlases of the marmoset brain are mainly based on 2D histological data, which are difficult to apply to 3D imaging techniques. Here, we constructed a 3D digital atlas based on high-resolution ex-vivo MRI images, including magnetization transfer ratio (a T1-like contrast), T2w images, and multi-shell diffusion MRI. Based on the multi-modal MRI images, we manually delineated 54 cortical areas and 16 subcortical regions on one hemisphere of the brain (the core version). The 54 cortical areas were merged into 13 larger cortical regions according to their locations to yield a coarse version of the atlas, and also parcellated into 106 sub-regions using a connectivity-based parcellation method to produce a refined atlas. Finally, we compared the new atlas set with existing histology atlases and demonstrated its applications in connectome studies, and in resting state and stimulus-based fMRI. The atlas set has been integrated into the widely-distributed neuroimaging data analysis software AFNI and SUMA, providing a readily usable multi-modal template space with multi-level anatomical labels (including labels from the Paxinos atlas) that can facilitate various neuroimaging studies of marmosets.

Zoonotic infection of Brazilian primate workers with New World simian foamy virus.

Simian foamy viruses (SFVs) are retroviruses present in nearly all nonhuman primates (NHPs), including Old World primates (OWP) and New World primates (NWP). While all confirmed human infections with SFV are from zoonotic transmissions originating from OWP, little is known about the zoonotic transmission potential of NWP SFV. We conducted a longitudinal, prospective study of 56 workers occupationally exposed to NWP in Brazil. Plasma from these workers was tested using Western blot (WB) assays containing NWP SFV antigens. Genomic DNA from blood and buccal swabs was analyzed for the presence of proviral SFV sequences by three nested PCR tests and a new quantitative PCR assay. Exposure histories were obtained and analyzed for associations with possible SFV infection. Ten persons (18%) tested seropositive and two persons were seroindeterminate (3.6%) for NWP SFV. Six persons had seroreactivity over 2–3 years suggestive of persistent infection. All SFV NWP WB-positive workers reported at least one incident involving NWP, including six reporting NWP bites. NWP SFV viral DNA was not detected in the blood or buccal swabs from all 12 NWP SFV seroreactive workers. We also found evidence of SFV seroreversion in three workers suggestive of possible clearance of infection. Our findings suggest that NWP SFV can be transmitted to occupationally-exposed humans and can elicit specific humoral immune responses but infection remains well-controlled resulting in latent infection and may occasionally clear.

Ancestral resurrection of anthropoid estrogen receptor β demonstrates functional consequences of positive selection

Anthropoid primates arose during the Eocene approximately 55 million years ago (mya), and extant anthropoids share a most recent common ancestor ∼40mya. Paleontology has been very successful at describing the morphological phenotypes of extinct anthropoids. Less well understood is the molecular biology of these extinct species as well as the phenotypic consequences of evolutionary variation in their genomes. Here we resurrect the most recent common ancestral anthropoid estrogen receptor β gene (ESR2) and demonstrate that the function of this ancestral estrogen receptor has been maintained during human descent but was altered during early New World monkey (NWM) evolution by becoming a more potent transcriptional activator. We tested hypotheses of adaptive evolution in the protein coding sequences of ESR2, and determined that ESR2 evolved via episodic positive selection on the NWM stem lineage. We separately co-transfected ESR2 constructs for human, NWM, and the anthropoid ancestor along with reporter gene vectors and performed hormone binding dose response experiments that measure transactivation activity. We found the transactivation potentials of the ancestral and human sequences to be significantly lower (p<0.0001 in each comparison) than that of the NWM when treated with estradiol, the most prevalent estrogen. We conclude the difference in fold activation is due to positive selection in the NWM ERβ ligand binding domain. Our study validates inferential methods for detecting adaptive evolution that predict functional consequences of nucleotide substitutions and points a way toward examining the functional consequences of positive Darwinian selection.