Person: Arnold, C
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Arnold
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Arnold, C
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Publication 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, CharlesBody 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.Publication Simulating Trait Evolution for Cross-Cultural Comparison(The Royal Society, 2010) Nunn, Charles; Arnold, C; Matthews, Luke; Borgerhoff Mulder, MoniqueCross-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 researchPublication Phylogenetic Targeting of Research Effort in Evolutionary Biology(University of Chicago Press, 2010) Arnold, C; Nunn, CharlesMany 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).Publication Polynomial Algorithms for the Maximal Pairing Problem: Efficient Phylogenetic Targeting on Arbitrary Trees(BioMed Central, 2010) Arnold, C; Stadler, Peter FBackground: The Maximal Pairing Problem (MPP) is the prototype of a class of combinatorial optimization problems that are of considerable interest in bioinformatics: Given an arbitrary phylogenetic tree T and weights ωxy for the paths between any two pairs of leaves (x, y), what is the collection of edge-disjoint paths between pairs of leaves that maximizes the total weight? Special cases of the MPP for binary trees and equal weights have been described previously; algorithms to solve the general MPP are still missing, however. Results: We describe a relatively simple dynamic programming algorithm for the special case of binary trees. We then show that the general case of multifurcating trees can be treated by interleaving solutions to certain auxiliary Maximum Weighted Matching problems with an extension of this dynamic programming approach, resulting in an overall polynomial-time solution of complexity (n^4 log n) w.r.t. the number n of leaves. The source code of a C implementation can be obtained under the GNU Public License from http://www.bioinf.uni-leipzig.de/Software/Targeting. For binary trees, we furthermore discuss several constrained variants of the MPP as well as a partition function approach to the probabilistic version of the MPP. Conclusions: The algorithms introduced here make it possible to solve the MPP also for large trees with high-degree vertices. This has practical relevance in the field of comparative phylogenetics and, for example, in the context of phylogenetic targeting, i.e., data collection with resource limitations.Publication The 10kTrees Website: A New Online Resource for Primate Phylogeny(John Wiley & Sons, 2010) Arnold, C; Matthews, Luke J.; Nunn, CharlesThe 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.Publication Mutualism or Parasitism? Using a Phylogenetic Approach to Characterize the Oxpecker-Ungulate Relationship(Wiley-Blackwell, 2011) Nunn, Charles; Ezenwa, Vanessa O.; Arnold, C; Koenig, Walter D.With their striking predilection for perching on African ungulates and eating their ticks, yellow-billed (Buphagus africanus) and red-billed oxpeckers (B. erythrorhynchus) represent one of the few potentially mutualistic relationships among vertebrates. The nature of the oxpecker–ungulate relationship remains uncertain, however, because oxpeckers are known to consume ungulate tissues, suggesting that the relationship between oxpeckers and ungulates may also be parasitic. To examine this issue further, we obtained data on oxpecker preferences for different ungulate species, the abundance of ticks on these ungulates, and ungulate hide thickness. In support of the mutualism hypothesis, we found that both species of oxpeckers prefer ungulate hosts that harbor a higher abundance of ticks. We found no evidence that hide thickness—a measure of the potential for parasitism by oxpeckers—predicts oxpecker preferences for different ungulate species. Oxpeckers also prefer larger-bodied ungulates, possibly because larger animals have more ticks, provide a more stable platform upon which to forage, or support more oxpeckers feeding simultaneously. However, the preference for ungulates with greater tick abundance was independent of host body mass. These results support the hypothesis that the relationship between oxpeckers and ungulates is primarily mutualistic.Publication Comparative Chewing Efficiency in Mammalian Herbivores(Nordic Ecological Society, 2009) Fritz, Julia; Hummel, Jürgen; Kienzle, Ellen; Arnold, C; Nunn, Charles; Clauss, MarcusAlthough the relevance of particle size reduction in herbivore digestion is widely appreciated, few studies have investigated digesta particle size across species in relation to body mass or digestive strategy. We investigated faecal particle size, which reflects the size of ingesta particles after both mastication and specialized processes such as rumination. Particle size was measured by wet sieving samples from more than 700 captive individuals representing 193 mammalian species. Using phylogenetic generalized least squares, faecal particle size scaled to body mass with an exponent of 0.22 (95% confidence interval: 0.16–0.28). In comparisons among different digestive strategies, we found that (1) equids had smaller faecal particles than other hindgut fermenters, (2) non-ruminant foregut fermenters and hindgut fermenters had similar-sized faecal particles (not significantly different), and (3) ruminants had finer faecal particles than non-ruminants. These results confirm that the relationship between chewing efficiency and body mass is modified by morphological adaptations in dental design and physiological adaptations to chewing, such as rumination. This allometric relationship should be considered when investigating the effect of body size on digestive physiology, and digestion studies should include a measure of faecal particle size.