100,205 research outputs found
A Composite Genome Approach to Identify Phylogenetically Informative Data from Next-Generation Sequencing
We have developed a novel method to rapidly obtain homologous genomic data
for phylogenetics directly from next-generation sequencing reads without the
use of a reference genome. This software, called SISRS, avoids the time
consuming steps of de novo whole genome assembly, genome-genome alignment, and
annotation. For simulations SISRS is able to identify large numbers of loci
containing variable sites with phylogenetic signal. For genomic data from apes,
SISRS identified thousands of variable sites, from which we produced an
accurate phylogeny. Finally, we used SISRS to identify phylogenetic markers
that we used to estimate the phylogeny of placental mammals. We recovered
phylogenies from multiple datasets that were consistent with previous
conflicting estimates of the relationships among mammals. SISRS is open source
and freely available at https://github.com/rachelss/SISRS.Comment: 12 pages plus36 figures, 1 supplementary table, 3 supplementary
figure
Generalized Buneman pruning for inferring the most parsimonious multi-state phylogeny
Accurate reconstruction of phylogenies remains a key challenge in
evolutionary biology. Most biologically plausible formulations of the problem
are formally NP-hard, with no known efficient solution. The standard in
practice are fast heuristic methods that are empirically known to work very
well in general, but can yield results arbitrarily far from optimal. Practical
exact methods, which yield exponential worst-case running times but generally
much better times in practice, provide an important alternative. We report
progress in this direction by introducing a provably optimal method for the
weighted multi-state maximum parsimony phylogeny problem. The method is based
on generalizing the notion of the Buneman graph, a construction key to
efficient exact methods for binary sequences, so as to apply to sequences with
arbitrary finite numbers of states with arbitrary state transition weights. We
implement an integer linear programming (ILP) method for the multi-state
problem using this generalized Buneman graph and demonstrate that the resulting
method is able to solve data sets that are intractable by prior exact methods
in run times comparable with popular heuristics. Our work provides the first
method for provably optimal maximum parsimony phylogeny inference that is
practical for multi-state data sets of more than a few characters.Comment: 15 page
The use of phylogeny to interpret cross-cultural patterns in plant use and guide medicinal plant discovery: an example from Pterocarpus (Leguminosae)
The study of traditional knowledge of medicinal plants has led to discoveries that have helped combat diseases and improve healthcare. However, the development of quantitative measures that can assist our quest for new medicinal plants has not greatly advanced in recent years. Phylogenetic tools have entered many scientific fields in the last two decades to provide explanatory power, but have been overlooked in ethnomedicinal studies. Several studies show that medicinal properties are not randomly distributed in plant phylogenies, suggesting that phylogeny shapes ethnobotanical use. Nevertheless, empirical studies that explicitly combine ethnobotanical and phylogenetic information are scarce.In this study, we borrowed tools from community ecology phylogenetics to quantify significance of phylogenetic signal in medicinal properties in plants and identify nodes on phylogenies with high bioscreening potential. To do this, we produced an ethnomedicinal review from extensive literature research and a multi-locus phylogenetic hypothesis for the pantropical genus Pterocarpus (Leguminosae: Papilionoideae). We demonstrate that species used to treat a certain conditions, such as malaria, are significantly phylogenetically clumped and we highlight nodes in the phylogeny that are significantly overabundant in species used to treat certain conditions. These cross-cultural patterns in ethnomedicinal usage in Pterocarpus are interpreted in the light of phylogenetic relationships.This study provides techniques that enable the application of phylogenies in bioscreening, but also sheds light on the processes that shape cross-cultural ethnomedicinal patterns. This community phylogenetic approach demonstrates that similar ethnobotanical uses can arise in parallel in different areas where related plants are available. With a vast amount of ethnomedicinal and phylogenetic information available, we predict that this field, after further refinement of the techniques, will expand into similar research areas, such as pest management or the search for bioactive plant-based compounds
Convergence and divergence in the evolution of cat skulls: temporal and spatial patterns of morphological diversity
Background: Studies of biological shape evolution are greatly enhanced when framed in a phylogenetic perspective.
Inclusion of fossils amplifies the scope of macroevolutionary research, offers a deep-time perspective on tempo and mode
of radiations, and elucidates life-trait changes. We explore the evolution of skull shape in felids (cats) through morphometric
analyses of linear variables, phylogenetic comparative methods, and a new cladistic study of saber-toothed cats.
Methodology/Principal Findings: A new phylogenetic analysis supports the monophyly of saber-toothed cats
(Machairodontinae) exclusive of Felinae and some basal felids, but does not support the monophyly of various sabertoothed
tribes and genera. We quantified skull shape variation in 34 extant and 18 extinct species using size-adjusted linear
variables. These distinguish taxonomic group membership with high accuracy. Patterns of morphospace occupation are
consistent with previous analyses, for example, in showing a size gradient along the primary axis of shape variation and a
separation between large and small-medium cats. By combining the new phylogeny with a molecular tree of extant Felinae,
we built a chronophylomorphospace (a phylogeny superimposed onto a two-dimensional morphospace through time). The
evolutionary history of cats was characterized by two major episodes of morphological divergence, one marking the
separation between saber-toothed and modern cats, the other marking the split between large and small-medium cats.
Conclusions/Significance: Ancestors of large cats in the ‘Panthera’ lineage tend to occupy, at a much later stage,
morphospace regions previously occupied by saber-toothed cats. The latter radiated out into new morphospace regions
peripheral to those of extant large cats. The separation between large and small-medium cats was marked by considerable
morphologically divergent trajectories early in feline evolution. A chronophylomorphospace has wider applications in
reconstructing temporal transitions across two-dimensional trait spaces, can be used in ecophenotypical and functional
diversity studies, and may reveal novel patterns of morphospace occupation
Temporal Phylogenetic Networks and Logic Programming
The concept of a temporal phylogenetic network is a mathematical model of
evolution of a family of natural languages. It takes into account the fact that
languages can trade their characteristics with each other when linguistic
communities are in contact, and also that a contact is only possible when the
languages are spoken at the same time. We show how computational methods of
answer set programming and constraint logic programming can be used to generate
plausible conjectures about contacts between prehistoric linguistic
communities, and illustrate our approach by applying it to the evolutionary
history of Indo-European languages.
To appear in Theory and Practice of Logic Programming (TPLP)
Evolutionary Inference for Function-valued Traits: Gaussian Process Regression on Phylogenies
Biological data objects often have both of the following features: (i) they
are functions rather than single numbers or vectors, and (ii) they are
correlated due to phylogenetic relationships. In this paper we give a flexible
statistical model for such data, by combining assumptions from phylogenetics
with Gaussian processes. We describe its use as a nonparametric Bayesian prior
distribution, both for prediction (placing posterior distributions on ancestral
functions) and model selection (comparing rates of evolution across a
phylogeny, or identifying the most likely phylogenies consistent with the
observed data). Our work is integrative, extending the popular phylogenetic
Brownian Motion and Ornstein-Uhlenbeck models to functional data and Bayesian
inference, and extending Gaussian Process regression to phylogenies. We provide
a brief illustration of the application of our method.Comment: 7 pages, 1 figur
Phylogenetic congruence between subtropical trees and their associated fungi.
Recent studies have detected phylogenetic signals in pathogen-host networks for both soil-borne and leaf-infecting fungi, suggesting that pathogenic fungi may track or coevolve with their preferred hosts. However, a phylogenetically concordant relationship between multiple hosts and multiple fungi in has rarely been investigated. Using next-generation high-throughput DNA sequencing techniques, we analyzed fungal taxa associated with diseased leaves, rotten seeds, and infected seedlings of subtropical trees. We compared the topologies of the phylogenetic trees of the soil and foliar fungi based on the internal transcribed spacer (ITS) region with the phylogeny of host tree species based on matK, rbcL, atpB, and 5.8S genes. We identified 37 foliar and 103 soil pathogenic fungi belonging to the Ascomycota and Basidiomycota phyla and detected significantly nonrandom host-fungus combinations, which clustered on both the fungus phylogeny and the host phylogeny. The explicit evidence of congruent phylogenies between tree hosts and their potential fungal pathogens suggests either diffuse coevolution among the plant-fungal interaction networks or that the distribution of fungal species tracked spatially associated hosts with phylogenetically conserved traits and habitat preferences. Phylogenetic conservatism in plant-fungal interactions within a local community promotes host and parasite specificity, which is integral to the important role of fungi in promoting species coexistence and maintaining biodiversity of forest communities
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