Characterization of a novel simian immunodeficiency virus from guereza colobus monkeys (Colobus guereza) in Cameroon: a new lineage in the nonhuman primate lentivirus family

Exploration of the diversity among primate lentiviruses is necessary to elucidate the origins and evolution of immunodeficiency viruses. During a serological survey in Cameroon, we screened 25 wild-born guereza colobus monkeys (Colobus guereza) and identified 7 with HIV/SIV cross-reactive antibodies. In this study, we describe a novel lentivirus, named SIVcol, prevalent in guereza colobus monkeys. Genetic analysis revealed that SIVcol was very distinct from all other known SIV/HIV isolates, with average amino acid identities of 40% for Gag, 50% for Pol, 28% for Env, and around 25% for proteins encoded by five other genes. Phylogenetic analyses confirmed that SIVcol is genetically distinct from other previously characterized primate lentiviruses and clusters independently, forming a novel lineage, the sixth in the current classification. Cercopithecidae monkeys (Old World monkeys) are subdivided into two subfamilies, the Colobinae and the Cercopithecinae, and, so far, all Cercopithecidae monkeys from which lentiviruses have been isolated belong to the Cercopithecinae subfamily. Therefore, SIVcol from guereza colobus monkeys (C. guereza) is the first primate lentivirus identified in the Colobinae subfamily and the divergence of SIVcol may reflect divergence of the host lineage.     

Complete nucleotide sequence of simian endogenous type D retrovirus with intact genome organization: evidence for ancestry to simian retrovirus and baboon endogenous virus.

A complete endogenous type D viral genome has been isolated from a baboon genomic library. The provirus, simian endogenous retrovirus (SERV), is 8,393 nucleotides long and contains two long terminal repeats and complete genes for gag, pro, pol, and env. The primer binding site is complementary to tRNA(Lys)3, like in lentiviruses. The env GP70 protein is highly homologous to that of baboon endogenous virus (BaEV). PCR analysis of primate DNA showed that related proviral sequences are present in Old World monkeys of the subfamily Cercopithecinae but not in apes and humans. Analysis of virus and host sequences indicated that the proviral genomes were inherited from a common ancestor. Comparison of the evolution of BaEV, exogenous simian retrovirus types 1 to 3 (SRV1 to SRV3), and SERV suggests that SERV is ancestral to both BaEV and the SRVs.     

Differences in the gut microbiota between Cercopithecinae and Colobinae in captivity

The gut microbiome of captive primates can provide a window into their health and disease status. The diversity and composition of gut microbiota are influenced by not only host phylogeny, but also host diet. Old World monkeys (Cercopithecidae) are divided into two subfamilies: Cercopithecinae and Colobinae. The diet and physiological digestive features differ between these two subfamilies. Accordingly, highthroughput sequencing was used to examine gut microbiota differences between these two subfamilies, using data from 29 Cercopithecinae individuals and 19 Colobinae individuals raised in captivity. Through a comparative analysis of operational taxonomic units (OTUs), significant differences in the diversity and composition of gut microbiota were observed between Cercopithecinae and Colobinae. In particular, the gut microbiota of captive Old World monkeys clustered strongly by the two subfamilies. The Colobinae microbial diversity was higher than that of Cercopithecinae. Additionally, Firmicutes, Lactobacillaceae, Veillonellaceae, and Prevotella abundance were higher in Cercopithecinae, while Bacteroidetes, Ruminococcaceae, Christensenellaceae, Bacteroidaceae, and Acidaminococcaceae abundance were higher in Colobinae. PICRUSt analysis revealed that the predicted metagenomes of metabolic pathways associated with proteins, carbohydrates, and amino acids were significantly higher in Colobinae. In the context of host phylogeny, these differences between Cercopithecinae and Colobinae could reflect adaptations associated with their respective diets. This well-organized dataset is a valuable resource for future related research on primates and gut microbiota. Moreover, this study may provide useful insight into animal management practices and primate conservation.

     

Comparative chromosome banding studies in the family Cercopithecidae

Comparative banding studies in eight species of the family Cercopithecidae, subfamily Cercopithecinae allowed us to identify the chromosomes that have been conserved and those that have undergone structural changes. The results suggest that while the ancestral karyotype of the Cercopithecini was probably similar to that ofCercopithecus aethiops, the ancestral complement of the cercopithecinae was probably of the type now found in the Papionini. Thus, after their divergence, one of the groups maintained an extremely stable chromosomal complement (Papionini 2n=42) while the other underwent extreme chromosomal rearrangements (Cercopithecini 2n=48–72).     

The ability of primate lentiviruses to degrade the monocyte restriction factor SAMHD1 preceded the birth of the viral accessory protein Vpx

The human SAMHD1 protein potently restricts lentiviral infection in dendritic cells and monocyte/macrophages but is antagonized by the primate lentiviral protein Vpx, which targets SAMHD1 for degradation. However, only two of eight primate lentivirus lineages encode Vpx, whereas its paralog, Vpr, is conserved across all extant primate lentiviruses. We find that not only multiple Vpx but also some Vpr proteins are able to degrade SAMHD1, and such antagonism led to dramatic positive selection of SAMHD1 in the primate subfamily Cercopithecinae. Residues that have evolved under positive selection precisely determine sensitivity to Vpx/Vpr degradation and alter binding specificity. By overlaying these functional analyses on a phylogenetic framework of Vpr and Vpx evolution, we can decipher the chronology of acquisition of SAMHD1-degrading abilities in lentiviruses. We conclude that vpr neofunctionalized to degrade SAMHD1 even prior to the birth of a separate vpx gene, thereby initiating an evolutionary arms race with SAMHD1.     

Cheek pouch use, predation risk, and feeding competition in blue monkeys (Cercopithecus mitis stuhlmanni)

The adaptive function of cheek pouches in the primate subfamily Cercopithecinae remains unresolved. By analyzing the circumstances of cheek pouch use, we tested two hypotheses for the evolution of cercopithecine cheek pouches proposed in earlier studies: (1) cheek pouches reduce vulnerability to predation, and (2) cheek pouches increase feeding efficiency by reducing competition. We studied two groups of wild blue monkeys (Cercopithecus mitis stuhlmanni) in the Kakamega Forest, Kenya, conducting focal observations of feeding individuals. Monkeys were less exposed while emptying their cheek pouches than filling them, supporting the predation-avoidance hypothesis. We investigated several measures of competitive threat, but only one supported the competition-reduction hypothesis: when the nearest neighbor's rank increased, subjects were more likely to increase than to decrease cheek pouch use. Overall, our findings supported the predation-avoidance hypothesis more strongly than the competition-reduction hypothesis. We suggest that variation in cheek pouch use may reflect differing behavioral strategies used by cercopithecines to mitigate competition and predation, as well as factors such as resource size and distribution, home range size, and travel patterns.     

Higher level phylogeny of Satyrinae butterflies (Lepidoptera: Nymphalidae) based on DNA sequence data

We have inferred the first empirically supported hypothesis of relationships for the cosmopolitan butterfly subfamily Satyrinae. We used 3090 base pairs of DNA from the mitochondrial gene COI and the nuclear genes EF-1alpha and wingless for 165 Satyrinae taxa representing 4 tribes and 15 subtribes, and 26 outgroups, in order to test the monophyly of the subfamily and elucidate phylogenetic relationships of its major lineages. In a combined analysis, the three gene regions supported an almost fully resolved topology, which recovered Satyrinae as polyphyletic, and revealed that the current classification of suprageneric taxa within the subfamily is comprised almost completely of unnatural assemblages. The most noteworthy findings are that Manataria is closely related to Melanitini; Palaeonympha belongs to Euptychiina; Oressinoma, Orsotriaena and Coenonympha group with the Hypocystina; Miller's (1968). Parargina is polyphyletic and its components group with multiple distantly related lineages; and the subtribes Elymniina and Zetherina fall outside the Satyrinae. The three gene regions used in a combined analysis prove to be very effective in resolving relationships of Satyrinae at the subtribal and tribal levels. Further sampling of the taxa closely related to Satyrinae, as well as more extensive sampling of genera within the tribes and subtribes for this group will be critical to test the monophyly of the subfamily and establish a stronger basis for future biogeographical and evolutionary studies.     

Consentaneous Agent-Based and Stochastic Model of the Financial Markets

We are looking for the agent-based treatment of the financial markets considering necessity to build bridges between microscopic, agent based, and macroscopic, phenomenological modeling. The acknowledgment that agent-based modeling framework, which may provide qualitative and quantitative understanding of the financial markets, is very ambiguous emphasizes the exceptional value of well defined analytically tractable agent systems. Herding as one of the behavior peculiarities considered in the behavioral finance is the main property of the agent interactions we deal with in this contribution. Looking for the consentaneous agent-based and macroscopic approach we combine two origins of the noise: exogenous one, related to the information flow, and endogenous one, arising form the complex stochastic dynamics of agents. As a result we propose a three state agent-based herding model of the financial markets. From this agent-based model we derive a set of stochastic differential equations, which describes underlying macroscopic dynamics of agent population and log price in the financial markets. The obtained solution is then subjected to the exogenous noise, which shapes instantaneous return fluctuations. We test both Gaussian and q-Gaussian noise as a source of the short term fluctuations. The resulting model of the return in the financial markets with the same set of parameters reproduces empirical probability and spectral densities of absolute return observed in New York, Warsaw and NASDAQ OMX Vilnius Stock Exchanges. Our result confirms the prevalent idea in behavioral finance that herding interactions may be dominant over agent rationality and contribute towards bubble formation.     

陕西蓝田公王岭“蓝田伟猴”化石的再研究

蓝田公王岭动物群中,唯一的一种非人灵长类化石由胡长康、齐陶(1978)定名为Megamacaca lantianensis(蓝田伟猴)。但按其形态,我们觉得把它归于疣猴亚科比较适宜。特别是与该亚科中的金丝猴属(Rhinopithecus)更为相像,例如蓝田标本下颌支与下颌体垂直,冠状突略向后弯,齿尖起伏较大等都显示了金丝猴的一般性质。至此,本文将蓝田伟猴归于金丝猴属,保留原有种名:Rhinopithecus(Megamacaca)lantianensis(Hu and Qi)。时代为早更新世晚期。     

An agent-based model of group decision making in baboons

We present an agent-based model of the key activities of a troop of chacma baboons (Papio hamadryas ursinus) based on the data collected at De Hoop Nature Reserve in South Africa. We analyse the predictions of the model in terms of how well it is able to duplicate the observed activity patterns of the animals and the relationship between the parameters that control the agent's decision procedure and the model's predictions. At the current stage of model development, we are able to show that across a wide range of decision parameter values, the baboons are able to achieve their energetic and social time requirements. The simulation results also show that decisions concerning movement (group action selection) have the greatest influence on the outcomes. Those cases where the model's predictions fail to agree with the observed activity patterns have highlighted key elements that were missing from the field data, and that would need to be collected in subsequent fieldwork. Based on our experience, we believe group decision making is a fertile field for future research, and agent-based modelling offers considerable scope for understanding group action selection.     

Group-Wise Herding Behavior in Financial Markets: An Agent-Based Modeling Approach

In this paper, we shed light on the dynamic characteristics of rational group behaviors and the relationship between monetary policy and economic units in the financial market by using an agent-based model (ABM), the Hurst exponent, and the Shannon entropy. First, an agent-based model is used to analyze the characteristics of the group behaviors at different levels of irrationality. Second, the Hurst exponent is applied to analyze the characteristics of the trend-following irrationality group. Third, the Shannon entropy is used to analyze the randomness and unpredictability of group behavior. We show that in a system that focuses on macro-monetary policy, steep fluctuations occur, meaning that the medium-level irrationality group has the highest Hurst exponent and Shannon entropy among all of the groups. However, in a system that focuses on micro-monetary policy, all group behaviors follow a stable trend, and the medium irrationality group thus remains stable, too. Likewise, in a system that focuses on both micro- and macro-monetary policies, all groups tend to be stable. Consequently, we find that group behavior varies across economic units at each irrationality level for micro- and macro-monetary policy in the financial market. Together, these findings offer key insights into monetary policy.     

A molecular phylogenetic study of southern African Apiaceae

It has been suggested that southern Africa is the origin of the predominantly herbaceous Apiaceae subfamily Apioideae and that the woody habit is plesiomorphic. We expand previous molecular phylogenetic analyses of the family by considering all but three of the approximately 38 genera native to southern Africa, including all genera whose members, save one, have a woody habit. Representatives of five other genera are included because they may be closely related to these southern African taxa. Chloroplast DNA rps16 intron and/or nuclear rDNA ITS sequences for 154 accessions are analyzed using maximum parsimony, Bayesian, and maximum likelihood methods. Within Apioideae, two major clades hitherto unrecognized in the subfamily are inferred. The monogeneric Lichtensteinia clade is sister group to all other members of the subfamily, whereas the Annesorhiza clade (Annesorhiza, Chamarea, and Itasina) plus Molopospermum (and Astydamia in the ITS trees) are the successive sister group to all Apioideae except Lichtensteinia. Tribe Heteromorpheae is expanded to include Pseudocarum, "Oreofraga" ined., and five genera endemic to Madagascar. The southern African origin of subfamily Apioideae is corroborated (with subsequent migration northward into Eurasia along two dispersal routes), and the positions of the herbaceous Lichtensteinia and Annesorhiza clades within the subfamily suggest, surprisingly, that its ancestor was herbaceous, not woody.     

Molecular systematics of Apiaceae subfamily Apioideae: phylogenetic analyses of nuclear ribosomal DNA internal transcribed spacer and plastid RPO C1 intron sequences

Evolutionary relationships among representatives of Apiaceae (Umbelliferae) subfamily Apioideae have been inferred from phylogenetic analyses of nuclear ribosomal DNA internal transcribed spacer (ITS 1 and ITS 2) and plastid rpoC1 intron sequences. High levels of nucleotide sequence variation preclude the use of the ITS region for examining relationships across subfamilial boundaries in Apiaceae, whereas the rpoC1 intron is more suitably conserved for family-wide phylogenetic study but is too conserved for examining relationships among closely related taxa. In total, 126 ITS sequences from subfamily Apioideae and 100 rpoC1 intron sequences from Apiaceae (all three subfamilies) and outgroups Araliaceae and Pittosporaceae were examined. Phylogenies estimated using parsimony, neighbor-joining, and maximum likelihood methods reveal that: (1) Apiaceae subfamily Apioideae is monophyletic and is sister group to Apiaceae subfamily Saniculoideae; (2) Apiaceae subfamily Hydrocotyloideae is not monophyletic, with some members strongly allied to Araliaceae and others to Apioideae + Saniculoideae; and (3) Apiaceae subfamily Apioideae comprises several well-supported subclades, but none of these coincide with previously recognized tribal divisions based largely on morphological and anatomical characters of the fruit. Four major clades in Apioideae are provisionally recognized and provide the framework for future lower level phylogenetic analyses. A putative secondary structure model of the Daucus carota (carrot) rpoC1 group II intron is presented. Of its six major structural domains, domains II and III are the most, and domains V and VI the least, variable.     

Modeling Imatinib-Treated Chronic Myelogenous Leukemia: Reducing the Complexity of Agent-Based Models

We develop a model for describing the dynamics of imatinib-treated chronic myelogenous leukemia. Our model is based on replacing the recent agent-based model of Roeder et al. (Nat. Med. 12(10):1181–1184, 2006) by a system of deterministic difference equations. These difference equations describe the time-evolution of clusters of individual agents that are grouped by discretizing the state space. Hence, unlike standard agent-base models, the complexity of our model is independent of the number of agents, which allows to conduct simulation studies with a realistic number of cells. This approach also allows to directly evaluate the expected steady states of the system. The results of our numerical simulations show that our model replicates the averaged behavior of the original Roeder model with a significantly reduced computational cost. Our general approach can be used to simplify other similar agent-based models. In particular, due to the reduced computational complexity of our technique, one can use it to conduct sensitivity studies of the parameters in large agent-based systems.     

Emergence of complex social networks from spatial structure and rules of thumb: a modelling approach

Individual-based computer models show that simple heuristic governing individuals’ behavior may suffice to generate complex patterns of social behavior at the group level such as those observed in animal societies. ‘GrooFiWorld’ is an example of such kind of computer models. In this model, self-organization and simple behavioral rules generate complex patterns of social behavior like those described in tolerant and intolerant societies of macaques. Social complexity results from the socio-spatial structure of the group, the nature of which is, in turn, a side-effect of intensity of aggression. The model suggests that a similar mechanism may give rise to complex social structures in macaques. It is, however, unknown if the spatial structure of the model and that of macaques are indeed similar. Here we used social networks analysis as a proxy for spatial structure of the group. Our findings show that the social networks of the model share similar qualitative features with those of macaques. As group size increases, the density and the average individual eigenvector centrality decrease and the modularity and centralization of the network increase. In social networks emerging from simulations resembling intolerant societies the density is lower, the modularity and centralization are higher, and the individuals ranking higher in the dominance hierarchy are more central than in the social networks emerging from simulations resembling egalitarian societies. Given the qualitative similarity between the social networks of the model and that of empirical data, our results suggest that the spatial structure of macaques is similar to that of the model. It seems thus plausible that, as in the model, the spatial structure combined with simple behavioral rules plays a role in the emergence of complex social networks and complex social behavior in macaques.     

The evolution of strong reciprocity: cooperation in heterogeneous populations

How do human groups maintain a high level of cooperation despite a low level of genetic relatedness among group members? We suggest that many humans have a predisposition to punish those who violate group-beneficial norms, even when this imposes a fitness cost on the punisher. Such altruistic punishment is widely observed to sustain high levels of cooperation in behavioral experiments and in natural settings. We offer a model of cooperation and punishment that we call STRONG RECIPROCITY: where members of a group benefit from mutual adherence to a social norm, strong reciprocators obey the norm and punish its violators, even though as a result they receive lower payoffs than other group members, such as selfish agents who violate the norm and do not punish, and pure cooperators who adhere to the norm but free-ride by never punishing. Our agent-based simulations show that, under assumptions approximating likely human environments over the 100000 years prior to the domestication of animals and plants, the proliferation of strong reciprocators when initially rare is highly likely, and that substantial frequencies of all three behavioral types can be sustained in a population. As a result, high levels of cooperation are sustained. Our results do not require that group members be related or that group extinctions occur.     

Diversity,Body Mass,and Latitudinal Gradients in Primates

We examined latitudinal gradients in central value and diversity of body mass of primates to increase understanding of the Forster effect (decrease in taxonomic diversity with increasing latitude) and the Bergmann effect (increase of body mass with latitude). Data are from the literature. We used species’ median body mass of females and mid-latitude (N = 164). We account for phylogenetic effects with comparative analysis by independent contrasts and analysis at differing taxonomic levels. Globally, diversity of both taxonomy and body mass declined significantly with increasing latitude. The decrease in the range of body masses with increasing latitude was caused mainly by the absence of several small-bodied clades at higher latitudes, but also by the absence there of great apes. The disappearance of the small-bodied clades caused an increase in median body mass with latitude, i.e., primates show a significant taxon-wide Bergmann effect, including with phylogenetic correction. Within the Primates, the Bergmann effect was significant within taxa that extend from the equator the farthest into temperate regions: the Old World infraorder Catarrhini, family Cercopithecidae, and subfamily Cercopithecinae; the Asian Cercopithecidae; and in Southeast Asian Sunda, Macaca. The results accord with hypotheses for the Forster effect that latitudinal gradients in taxonomic diversity result from high rates of speciation in the tropics, and ecological, and therefore evolutionary, constraints on diversity at higher latitudes. For the Bergmann effect, the results support energetic hypotheses that the very largest-bodied and the small-bodied taxa cannot survive the long periods of limited resources at higher latitudes.     

A hybrid agent-based approach for modeling microbiological systems

Models for systems biology commonly adopt Differential Equations or Agent-Based modeling approaches for simulating the processes as a whole. Models based on differential equations presuppose phenomenological intracellular behavioral mechanisms, while models based on Multi-Agent approach often use directly translated, and quantitatively less precise if-then logical rule constructs. We propose an extendible systems model based on a hybrid agent-based approach where biological cells are modeled as individuals (agents) while molecules are represented by quantities. This hybridization in entity representation entails a combined modeling strategy with agent-based behavioral rules and differential equations, thereby balancing the requirements of extendible model granularity with computational tractability. We demonstrate the efficacy of this approach with models of chemotaxis involving an assay of 10³ cells and 1.2×10⁶ molecules. The model produces cell migration patterns that are comparable to laboratory observations.     

Ecosystem engineering as an energy transfer process: a simple agent-based model

Ecosystem engineers are defined as organisms who modulate the availability of resources for themselves and other organisms by physically changing the environment. Ecosystem engineering is a well-recognised ecological interaction, but there is a limited number of general models due to the recent development of the field. Agent-based models are often used to study how organisms respond to changing environments and are suitable for modelling ecosystem engineering. To our knowledge, agent-based methodology has not yet been used to model ecosystem engineering. In this paper, we develop a simple agent-based population dynamics model of ecosystem engineering as an energy transfer process. We apply energy budget approach to conceptually explain how ecosystem engineers transfer energy to the environment and define various types of energy transfers relative to their effects on the engineers and other organisms. We simulate environments with various levels of resource abundance and compare the results of the model without ecosystem engineering agents to the model with ecosystem engineering agents. We find that in environments with higher levels of resources, the presence of ecosystem engineers increases the average carrying capacity and the strength of population fluctuations, while in environments with lower levels of resources, ecosystem engineering mitigates fluctuations, increases average carrying capacity and makes environments more resilient. Finally, we discuss about the further application of agent-based modelling for the theoretical and experimental development of the ecosystem engineering concept.