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53 results for “phylogenetic network”
Supplementary information for: Using networks to identify structure in phylogenetic tree sets
<p>Modern phylogenomic studies produce large sets of trees that can represent variation in inferred phylogenies across genes, uncertainty in estimated phylogenies for a given gene, or both. Standard practice is to condense this variation down to a small set of point estimates or consensus trees in order to facilitate display and interpretation. However, doing so results in the loss of enormous amounts of information about the structure of the underlying tree set. Here, we propose new approaches to explore and detect structure in the tree set itself. These approaches rely on the well-developed mathematical foundations of community detection in networks and leverage two different network types. The first type uses nodes to represent trees and connects these nodes with edges whose weights are determined by the similarity (affinity) of the trees. The second type uses nodes to represent bipartitions and connects nodes with edges whose weights represent the covariance in bipartition presence/absence across trees in the set. These two network types carry information that is complementary, but not identical. A variety of methods may be applied to both networks in order to identify interesting community structure. These community detection approaches provide a rich view of the information contained in phylogenomic data sets and facilitate investigation into the forces driving inferred phylogenetic variation across genomes.</p>
Data from: Phylogenetic signal in module composition and species connectivity in compartmentalized host-parasite networks
Across different taxa, networks of mutualistic or antagonistic interactions show consistent architecture. Most networks are modular, with modules being distinct species subsets connected mainly with each other and having few connections to other modules. We investigate the phylogenetic relatedness of species within modules and whether a phylogenetic signal is detectable in the within- and among module connectivity of species using 27 mammal-flea networks from the Palaearctic. In the 24 networks that were modular, closely-related hosts co-occurred in the same module more often than expected by chance; in contrast, this was rarely the case for parasites. The within- and among-module connectivity of the same host or parasite species varied geographically. However, among-module but not within-module connectivity of host and parasites was somewhat phylogenetically constrained. These findings suggest that the establishment of host-parasite networks results from the interplay between phylogenetic influences acting mostly on hosts and local factors acting on parasites, to create an asymmetrically constrained pattern of geographic variation in modular structure. Modularity in host-parasite networks seems to result from the shared evolutionary history of hosts and by trait convergence among unrelated parasites. This suggests profound differences between hosts and parasites in the establishment and functioning of bipartite antagonistic networks.
Data from: Quantifying species contributions to ecosystem processes: a global assessment of functional trait and phylogenetic metrics across avian seed-dispersal networks
Quantifying the role of biodiversity in ecosystems not only requires understanding the links between species and the ecological functions and services they provide, but also how these factors relate to measurable indices, such as functional traits and phylogenetic diversity. However, these relationships remain poorly understood, especially for heterotrophic organisms within complex ecological networks. Here, we assemble data on avian traits across a global sample of mutualistic plant–frugivore networks to critically assess how the functional roles of frugivores are associated with their intrinsic traits, as well as their evolutionary and functional distinctiveness. We find strong evidence for niche complementarity, with phenotypically and phylogenetically distinct birds interacting with more unique sets of plants. However, interaction strengths—the number of plant species dependent on a frugivore—were unrelated to evolutionary or functional distinctiveness, largely because distinct frugivores tend to be locally rare, and thus have fewer connections across the network. Instead, interaction strengths were better predicted by intrinsic traits, including body size, gape width and dietary specialization. Our analysis provides general support for the use of traits in quantifying species ecological functions, but also highlights the need to go beyond simple metrics of functional or phylogenetic diversity to consider the multiple pathways through which traits may determine ecological processes.
Data from: Manifold influences of phylogenetic structure on a plant-herbivore network
Ecologists are increasingly aware of the interplay between evolutionary history and ecological processes in shaping current species interaction patterns. The inclusion of phylogenetic relationships in studies of species interaction networks has shown that closely related species commonly interact with sets of similar species. Notably, the degree of phylogenetic conservatism in antagonistic ecological interactions is frequently stronger among species at lower trophic levels than among those at higher trophic levels. One hypothesis that accounts for this asymmetry is that competition among consumer species promotes resource partitioning and offsets the maintenance of dietary similarity by phylogenetic inertia. Here, we used a regional plant-herbivore network comprised of Asteraceae species and flower-head endophagous insects to evaluate how the strength of phylogenetic conservatism in species interactions differs between the two trophic levels. We also addressed whether the asymmetry in the strength of the phylogenetic signal between plants and animals depends on the overall degree of relatedness among the herbivores. We show that, beyond the previously reported compositional similarity, closely related species also share a greater proportion of counterpart phylogenetic history, both for resource and consumer species. Comparison of the patterns found in the entire network with those found in subnetworks composed of more phylogenetically restricted groups of herbivores provides evidence that resource partitioning occurs mostly at deeper phylogenetic levels, so that a positive phylogenetic signal in antagonist similarity is detectable even between closely related consumers in monophyletic subnetworks. The asymmetry in signal strength between trophic levels is most apparent in the way network modules reflect resource phylogeny, both for the entire network and for subnetworks. Taken together, these results suggest that evolutionary processes, such as phylogenetic conservatism and independent colonization history of the insect groups may be the main forces generating the phylogenetic structure observed in this particular plant–herbivore network system.
Data from: The contribution of rare species to community phylogenetic diversity across a global network of forest plots
Niche differentiation has been proposed as an explanation for rarity in species assemblages. Testing this hypothesis requires quantifying the ecological similarity of species. This similarity can potentially be estimated by using phylogenetic relatedness. In this study, we predicted that if niche differentiation does explain the co-occurrence of rare and common species, then rare species should contribute greatly to the overall community phylogenetic diversity (PD), abundance will have phylogenetic signal and that common and rare species will be phylogenetically dissimilar. We tested these predictions by developing a novel method that integrates species rank abundance distributions with phylogenetic trees and trend analyses to examine the relative contribution of individual species to the overall community PD. We then supplement this approach with analyses of phylogenetic signal in abundances and measures of phylogenetic similarity within and between rare and common species groups. We applied this analytical approach to 15 long-term temperate and tropical forest dynamics plots from around the world. We show that the niche differentiation hypothesis is supported in six forests but is rejected in nine forests, and that the three metrics utilized in this study each provide unique but corroborating information regarding the phylogenetic distribution of rarity in communities.
FIGURE. TCS network inferred from ITS1 in Morphological and phylogenetic relations of members of the genus Coelastrella (Scenedesmaceae, Chlorophyta) from the Ural and Khentii Mountains (Russia, Mongolia)
FIGURE. TCS network inferred from ITS1 Coelastrella sequences. The area of a circle is proportional to the number of Coelastrella sequences available in GenBank database. Mutational events between haplotypes are indicated by hatch marks at branches. The network was inferred using the algorithm described by Clement et al. (2002).
Lpnet: Reconstructing phylogenetic networks from distances using integer linear programming
<p>We present Lpnet, a variant of the widely used Neighbor-net method that approximates pairwise distances between taxa by a circular phylogenetic network. We first apply standard methods to construct a binary phylogenetic tree and then use integer linear programming to compute optimal circular orderings that agree with all tree splits. This approach achieves an improved approximation of the input distance for the clear majority of experiments that we have run for simulated and real data. We release an implementation in R that can handle up to 94 taxa and usually needs about one minute on a standard computer for 80 taxa. For larger taxa sets, we include a top-down heuristic which also tends to perform better than Neighbor-net.</p>
FIGURE 1. Phylogenetic relationship between Metarhizium synnematis GZUHXCHL12 in Delimitation of a novel member of genus Metarhizium (Clavicipitaceae) by phylogenetic and network analysis
FIGURE 1. Phylogenetic relationship between Metarhizium synnematis GZUHXCHL12 and its allies based on ITS-5.8S rDNA sequence data. Bootstrap values (1,000 replicates) are indicated above the nodes.
FIGURE 3 in Delimitation of a novel member of genus Metarhizium (Clavicipitaceae) by phylogenetic and network analysis
FIGURE 3. Metarhizium synnematis (holotype) A. Synnema on a lepidopteran cocoon. B. Upper part of a synnema. C. Phialides covering the surface of the synnema in a hymenium with conidia aggregating in sticky masses. D. Phialides. E. Conidia. Scale bars: A = 10 mm, B = 100 μm, C–E = 10 μm.
FIGURE 2 in Delimitation of a novel member of genus Metarhizium (Clavicipitaceae) by phylogenetic and network analysis
FIGURE 2. Minimum spanning network displaying the relationship among Metarhizium synnematis, Neotyphodium sp., Akanthomyces sp. and Metarhizium sp.
FIGURE 2. A phylogenetic network for a hypothetical data set. This network represents the relationships between four taxa, A-D in Exploring character conflict in molecular data*
FIGURE 2. A phylogenetic network for a hypothetical data set. This network represents the relationships between four taxa, A-D. The length of branch (a) is proportional to the strength of support for the relationship (A,C)(B,D). The length of branch (b) is proportional to the strength of support for the relationship (A,B)(C,D). In this example there is conflicting support for both of these arrangements, but more weight is given to (A,C)(B,D) than to (A,B)(C,D).
Dataset for "Exploring the distribution of phylogenetic networks generated under a birth-death-hybridization process"
<p>Contains all simulation scripts, simulated data, and supplemental materials</p>
Data from: Quantifying species contributions to ecosystem processes: a global assessment of functional trait and phylogenetic metrics across avian seed-dispersal networks
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Data from: Phylogenetic signal in module composition and species connectivity in compartmentalized host-parasite networks
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Lpnet: Reconstructing phylogenetic networks from distances using integer linear programming
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Supplementary information for: Using networks to identify structure in phylogenetic tree sets
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Data from: Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis
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Data from: Manifold influences of phylogenetic structure on a plant-herbivore network
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Data from: The contribution of rare species to community phylogenetic diversity across a global network of forest plots
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Data from: Maximum parsimony inference of phylogenetic networks in the presence of polyploid complexes
<p>Phylogenetic networks provide a powerful framework for modeling and analyzing reticulate evolutionary histories. While polyploidy has been shown to be prevalent not only in plants but also in other groups of eukaryotic species, most work done thus far on phylogenetic network inference assumes diploid hybridization. These inference methods have been applied, with varying degrees of success, to data sets with polyploid species, even though polyploidy violates the mathematical assumptions underlying these methods. Statistical methods were developed recently for handling specific types of polyploids and so were parsimony methods that could handle polyploidy more generally yet while excluding processes such as incomplete lineage sorting.</p> <p>In this paper, we introduce a new method for inferring most parsimonious phylogenetic networks on data that include polyploid species. Taking gene trees as input, the method seeks a phylogenetic network that minimizes deep coalescences while accounting for polyploidy. The method could also infer trees, thus potentially distinguishing between auto- and allo-polyploidy. We demonstrate the performance of the method on both simulated and biological data. The inference method as well as a method for evaluating given phylogenetic networks are implemented and publicly available in the PhyloNet software package.</p>
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