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Nunn, Charles

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Charles

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Nunn, Charles
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Now showing 1 - 10 of 32
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    Primate Extinction Risk and Historical Patterns of Speciation and Extinction in Relation to Body Mass
    (Royal Society of London, 2011) Matthews, Luke J.; Arnold, C; Machanda, Zarin; Nunn, Charles
    Body mass is thought to influence diversification rates, but previous studies have produced ambiguous results. We investigated patterns of diversification across 100 trees obtained from a new Bayesian inference of primate phylogeny that sampled trees in proportion to their posterior probabilities. First, we used simulations to assess the validity of previous studies that used linear models to investigate the links between IUCN Red List status and body mass. These analyses support the use of linear models for ordinal ranked data on threat status, and phylogenetic generalized linear models revealed a significant positive correlation between current extinction risk and body mass across our tree block. We then investigated historical patterns of speciation and extinction rates using a recently developed maximum-likelihood method. Specifically, we predicted that body mass correlates positively with extinction rate because larger bodied organisms reproduce more slowly, and body mass correlates negatively with speciation rate because smaller bodied organisms are better able to partition niche space. We failed to find evidence that extinction rates covary with body mass across primate phylogeny. Similarly, the speciation rate was generally unrelated to body mass, except in some tests that indicated an increase in the speciation rate with increasing body mass. Importantly, we discovered that our data violated a key assumption of sample randomness with respect to body mass. After correcting for this bias, we found no association between diversification rates and mass.
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    Host Longevity and Parasite Species Richness in Mammals
    (Public Library of Science, 2012-07-20) Cooper, Natalie; Kamilar, Jason; Nunn, Charles
    Hosts and parasites co-evolve, with each lineage exerting selective pressures on the other. Thus, parasites may influence host life-history characteristics, such as longevity, and simultaneously host life-history may influence parasite diversity. If parasite burden causes increased mortality, we expect a negative association between host longevity and parasite species richness. Alternatively, if long-lived species represent a more stable environment for parasite establishment, host longevity and parasite species richness may show a positive association. We tested these two opposing predictions in carnivores, primates and terrestrial ungulates using phylogenetic comparative methods and controlling for the potentially confounding effects of sampling effort and body mass. We also tested whether increased host longevity is associated with increased immunity, using white blood cell counts as a proxy for immune investment. Our analyses revealed weak relationships between parasite species richness and longevity. We found a significant negative relationship between longevity and parasite species richness for ungulates, but no significant associations in carnivores or primates. We also found no evidence for a relationship between immune investment and host longevity in any of our three groups. Our results suggest that greater parasite burden is linked to higher host mortality in ungulates. Thus, shorter-lived ungulates may be more vulnerable to disease outbreaks, which has implications for ungulate conservation, and may be applicable to other short-lived mammals.
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    Community Structure and the Spread of Infectious Disease in Primate Social Networks
    (Springer Netherlands, 2011) Griffin, Randi Heesoo; Nunn, Charles
    Living in a large social group is thought to increase disease risk in wild animal populations, but comparative studies have provided mixed support for this prediction. Here, we take a social network perspective to investigate whether patterns of social contact within groups influence parasite risk. Specifically, increased modularity (i.e. sub-grouping) in larger groups could offset the increased disease risk associated with living in a large group. We simulated the spread of a contagious pathogen in random social networks to generate theoretically grounded predictions concerning the relationship between social network connectivity and the success of socially transmitted pathogens. Simulations yielded the prediction that community modularity (Q) negatively impacts parasite success. No clear predictions emerged for a second network metric we considered, the eigenvector centralization index (C), as the relationship between this measure and parasite success depended on the transmission probability of parasites. We then tested the prediction that Q reduces parasite success in a phylogenetic comparative analysis of social network modularity and parasite richness across 19 primate species. Using a Bayesian implementation of phylogenetic generalized least squares and controlling for sampling effort, we found that primates living in larger groups exhibited higher Q, and as predicted by our simulations, higher Q was associated with lower richness of socially transmitted parasites. This suggests that increased modularity mediates the elevated risk of parasitism associated with living in larger groups, which could contribute to the inconsistent findings of empirical studies on the association between group size and parasite risk. Our results indicate that social networks may play a role in mediating pressure from socially transmitted parasites, particularly in large groups where opportunities for transmitting communicable diseases are abundant. We propose that parasite pressure in gregarious primates may have favored the evolution of behaviors that increase social network modularity, especially in large social groups.
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    Stepwise Model Fitting and Statistical Inference: Turning Noise into Signal Pollution
    (University of Chicago Press, 2009) Mundry, Roger; Nunn, Charles
    Statistical inference based on stepwise model selection is applied regularly in ecological, evolutionary, and behavioral research. In addition to fundamental shortcomings with regard to finding the “best” model, stepwise procedures are known to suffer from a multiple‐testing problem, yet the method is still widely used. As an illustration of this problem, we present results of a simulation study of artificial data sets of uncorrelated variables, with two to 10 predictor variables and one dependent variable. We then compared results from stepwise regression with a regression model in which all predictor variables were entered simultaneously. These analyses clearly demonstrate that significance tests based on stepwise procedures lead to greatly inflated Type I error rates (i.e., the probability of erroneously rejecting a true null hypothesis). By using a simple simulation design, our study amplifies previous warnings about using stepwise procedures, and we follow others in recommending that biologists refrain from applying these methods.
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    Simulating Trait Evolution for Cross-Cultural Comparison
    (The Royal Society, 2010) Nunn, Charles; Arnold, C; Matthews, Luke; Borgerhoff Mulder, Monique
    Cross-cultural anthropologists have increasingly used phylogenetic methods to study cultural variation. Because cultural behaviors can be transmitted horizontally among socially defined groups, however, it is important to assess whether phylogeny-based methods – which were developed to study vertically transmitted traits among biological taxa – are appropriate for studying group-level cultural variation. Here, we describe a spatially-explicit simulation model that can be used to generate data with known degrees of horizontal donation. We review previous results from this model showing that horizontal transmission increases the Type I error rate of phylogenetically independent contrasts in studies of correlated evolution. These conclusions apply to cases in which two traits are transmitted as a pair, but horizontal transmission may be less problematic when traits are unlinked. We also use the simulation model to investigate whether measures of homology (the consistency index and retention index) can detect horizontal transmission of cultural traits. Higher rates of evolutionary change have a stronger depressive impact on measures of homology than higher rates of horizontal transmission; thus, low consistency or retention indices are not necessarily indicative of “ethnogenesis.” Collectively, these studies demonstrate the importance of using simulations to assess the validity of methods in cross-cultural research
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    Phylogenetic Targeting of Research Effort in Evolutionary Biology
    (University of Chicago Press, 2010) Arnold, C; Nunn, Charles
    Many questions in comparative biology require that new data be collected, either to build a comparative database for the first time or to augment existing data. Given resource limitations in collecting data, the question arises as to which species should be studied to increase the size of comparative data sets. By taking hypotheses, existing data relevant to the hypotheses, and a phylogeny, we show that a method of “phylogenetic targeting” can systematically guide data collection while taking into account potentially confounding variables and competing hypotheses. Phylogenetic targeting selects potential candidates for future data collection, using a flexible scoring system based on differences in pairwise comparisons. We used simulations to assess the performance of phylogenetic targeting, as compared with the less systematic approach of randomly selecting species (as might occur when data have been collected without regard to phylogeny and variation in the traits of interest). The simulations revealed that phylogenetic targeting increased the statistical power to detect correlations and that power increased with the number of species in the tree, even when the number of species studied was held constant. We also developed a Web‐based computer program called PhyloTargeting to implement the approach (http://phylotargeting.fas.harvard.edu).
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    Investigating the Impact of Observation Errors on the Statistical Performance of Network-based Diffusion Analysis
    (Springer Verlag, 2010) Franz, Mathias; Nunn, Charles
    Experiments in captivity have provided evidence for social learning, but it remains challenging to demon- strate social learning in the wild. Recently, we developed network-based diffusion analysis (NBDA; 2009) as a new approach to inferring social learning from observational data. NBDA fits alternative models of asocial and social learning to the diffusion of a behavior through time, where the potential for social learning is related to a social network. Here, we investigate the performance of NBDA in relation to variation in group size, network heterogeneity, observer sampling errors, and duration of trait diffusion. We find that observation errors, when severe enough, can lead to increased Type I error rates in detecting social learning. However, elevated Type I error rates can be prevented by coding the observed times of trait acquisition into larger time units. Collectively, our results provide further guidance to applying NBDA and demonstrate that the method is more robust to sampling error than initially expected. Supplemental materials for this article may be downloaded from http:// lb.psychonomic-journals.org/content/supplemental.
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    Examining Landscape Factors Influencing Relative Distribution of Mosquito Genera and Frequency of Virus Infection
    (Springer Verlag, 2009) Junglen, S.; Kurth, A.; Kuehl, H.; Quan, P. L.; Ellerbrok, H.; Pauli, G.; Nitsche, A.; Nunn, Charles; Rich, S. M.; Lipkin, W. I.; Briese, T.; Leendertz, F. H.
    Mosquito-borne infections cause some of the most debilitating human diseases, including yellow fever and malaria, yet we lack an understanding of how disease risk scales with human-driven habitat changes. We present an approach to study variation in mosquito distribution and concomitant viral infections on the landscape level. In a pilot study we analyzed mosquito distribution along a 10-km transect of a West African rainforest area, which included primary forest, secondary forest, plantations, and human settlements. Variation was observed in the abundance of Anopheles, Aedes, Culex, and Uranotaenia mosquitoes between the different habitat types. Screening of trapped mosquitoes from the different habitats led to the isolation of five uncharacterized viruses of the families Bunyaviridae, Coronaviridae, Flaviviridae, and Rhabdoviridae, as well as an unclassified virus. Polymerase chain reaction screening for these five viruses in individual mosquitoes indicated a trend toward infection with specific viruses in specific mosquito genera that differed by habitat. Based on these initial analyses, we believe that further work is indicated to investigate the impact of anthropogenic landscape changes on mosquito distribution and accompanying arbovirus infection.
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    Sexual Dimorphism in Primate Aerobic Capacity: A Phylogenetic Test
    (John Wiley & Sons, 2010) Lindenfors, P.; Revell, L.J.; Nunn, Charles
    Male intrasexual competition should favour increased male physical prowess. This should in turn result in greater aerobic capacity in males than in females (i.e. sexual dimorphism) and a correlation between sexual dimorphism in aerobic capacity and the strength of sexual selection among species. However, physiological scaling laws predict that aerobic capacity should be lower per unit body mass in larger than in smaller animals, potentially reducing or reversing the sex difference and its association with measures of sexual selection. We used measures of haematocrit and red blood cell (RBC) counts from 45 species of primates to test four predictions related to sexual selection and body mass: (i) on average, males should have higher aerobic capacity than females, (ii) aerobic capacity should be higher in adult than juvenile males, (iii) aerobic capacity should increase with increasing sexual selection, but also that (iv) measures of aerobic capacity should co-vary negatively with body mass. For the first two predictions, we used a phylogenetic paired t-test developed for this study. We found support for predictions (i) and (ii). For prediction (iii), however, we found a negative correlation between the degree of sexual selection and aerobic capacity, which was opposite to our prediction. Prediction (iv) was generally supported. We also investigated whether substrate use, basal metabolic rate and agility influenced physiological measures of oxygen transport, but we found only weak evidence for a correlation between RBC count and agility.
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    The 10kTrees Website: A New Online Resource for Primate Phylogeny
    (John Wiley & Sons, 2010) Arnold, C; Matthews, Luke J.; Nunn, Charles
    The comparative method plays a central role in efforts to uncover the adaptive basis for primate behaviors, morphological traits, and cognitive abilities.[1-4] The comparative method has been used, for example, to infer that living in a larger group selects for a larger neocortex,[5][6] that primate territoriality favors a longer day range relative to home range size,[7] and that sperm competition can account for the evolution of primate testes size.[8][9] Comparison is fundamental for reconstructing behavioral traits in the fossil record, for example, in studies of locomotion and diet.[10-13] Recent advances in comparative methods require phylogenetic information,[2][14-16] but our knowledge of phylogenetic information is imperfect. In the face of uncertainty about evolutionary relationships, which phylogeny should one use? Here we provide a new resource for comparative studies of primates that enables users to run comparative analyses on multiple primate phylogenies Importantly, the 10,000 trees that we provide are not random, but instead use recent systematic methods to create a plausible set of topologies that reflect our certainty about some nodes on the tree and uncertainty about other nodes, given the dataset. The trees also reflect uncertainty about branch lengths.