21 research outputs found
Spatial Guilds in the Serengeti Food Web Revealed by a Bayesian Group Model
Food webs, networks of feeding relationships among organisms, provide
fundamental insights into mechanisms that determine ecosystem stability and
persistence. Despite long-standing interest in the compartmental structure of
food webs, past network analyses of food webs have been constrained by a
standard definition of compartments, or modules, that requires many links
within compartments and few links between them. Empirical analyses have been
further limited by low-resolution data for primary producers. In this paper, we
present a Bayesian computational method for identifying group structure in food
webs using a flexible definition of a group that can describe both functional
roles and standard compartments. The Serengeti ecosystem provides an
opportunity to examine structure in a newly compiled food web that includes
species-level resolution among plants, allowing us to address whether groups in
the food web correspond to tightly-connected compartments or functional groups,
and whether network structure reflects spatial or trophic organization, or a
combination of the two. We have compiled the major mammalian and plant
components of the Serengeti food web from published literature, and we infer
its group structure using our method. We find that network structure
corresponds to spatially distinct plant groups coupled at higher trophic levels
by groups of herbivores, which are in turn coupled by carnivore groups. Thus
the group structure of the Serengeti web represents a mixture of trophic guild
structure and spatial patterns, in contrast to the standard compartments
typically identified in ecological networks. From data consisting only of nodes
and links, the group structure that emerges supports recent ideas on spatial
coupling and energy channels in ecosystems that have been proposed as important
for persistence.Comment: 28 pages, 6 figures (+ 3 supporting), 2 tables (+ 4 supporting
A nonparametric HMM for genetic imputation and coalescent inference
Genetic sequence data are well described by hidden Markov models (HMMs) in
which latent states correspond to clusters of similar mutation patterns. Theory
from statistical genetics suggests that these HMMs are nonhomogeneous (their
transition probabilities vary along the chromosome) and have large support for
self transitions. We develop a new nonparametric model of genetic sequence
data, based on the hierarchical Dirichlet process, which supports these self
transitions and nonhomogeneity. Our model provides a parameterization of the
genetic process that is more parsimonious than other more general nonparametric
models which have previously been applied to population genetics. We provide
truncation-free MCMC inference for our model using a new auxiliary sampling
scheme for Bayesian nonparametric HMMs. In a series of experiments on male X
chromosome data from the Thousand Genomes Project and also on data simulated
from a population bottleneck we show the benefits of our model over the popular
finite model fastPHASE, which can itself be seen as a parametric truncation of
our model. We find that the number of HMM states found by our model is
correlated with the time to the most recent common ancestor in population
bottlenecks. This work demonstrates the flexibility of Bayesian nonparametrics
applied to large and complex genetic data
Distance Dependent Chinese Restaurant Processes
We develop the distance dependent Chinese restaurant process (CRP), a
flexible class of distributions over partitions that allows for
non-exchangeability. This class can be used to model many kinds of dependencies
between data in infinite clustering models, including dependencies across time
or space. We examine the properties of the distance dependent CRP, discuss its
connections to Bayesian nonparametric mixture models, and derive a Gibbs
sampler for both observed and mixture settings. We study its performance with
three text corpora. We show that relaxing the assumption of exchangeability
with distance dependent CRPs can provide a better fit to sequential data. We
also show its alternative formulation of the traditional CRP leads to a
faster-mixing Gibbs sampling algorithm than the one based on the original
formulation
Haplotype inference in crossbred populations without pedigree information
<p>Abstract</p> <p>Background</p> <p>Current methods for haplotype inference without pedigree information assume random mating populations. In animal and plant breeding, however, mating is often not random. A particular form of nonrandom mating occurs when parental individuals of opposite sex originate from distinct populations. In animal breeding this is called <it>crossbreeding </it>and <it>hybridization </it>in plant breeding. In these situations, association between marker and putative gene alleles might differ between the founding populations and origin of alleles should be accounted for in studies which estimate breeding values with marker data. The sequence of alleles from one parent constitutes one haplotype of an individual. Haplotypes thus reveal allele origin in data of crossbred individuals.</p> <p>Results</p> <p>We introduce a new method for haplotype inference without pedigree that allows nonrandom mating and that can use genotype data of the parental populations and of a crossbred population. The aim of the method is to estimate line origin of alleles. The method has a Bayesian set up with a Dirichlet Process as prior for the haplotypes in the two parental populations. The basic idea is that only a subset of the complete set of possible haplotypes is present in the population.</p> <p>Conclusion</p> <p>Line origin of approximately 95% of the alleles at heterozygous sites was assessed correctly in both simulated and real data. Comparing accuracy of haplotype frequencies inferred with the new algorithm to the accuracy of haplotype frequencies inferred with PHASE, an existing algorithm for haplotype inference, showed that the DP algorithm outperformed PHASE in situations of crossbreeding and that PHASE performed better in situations of random mating.</p
A hierarchical Dirichlet process mixture model for haplotype reconstruction from multi-population data
The perennial problem of "how many clusters?" remains an issue of substantial
interest in data mining and machine learning communities, and becomes
particularly salient in large data sets such as populational genomic data where
the number of clusters needs to be relatively large and open-ended. This
problem gets further complicated in a co-clustering scenario in which one needs
to solve multiple clustering problems simultaneously because of the presence of
common centroids (e.g., ancestors) shared by clusters (e.g., possible descents
from a certain ancestor) from different multiple-cluster samples (e.g.,
different human subpopulations). In this paper we present a hierarchical
nonparametric Bayesian model to address this problem in the context of
multi-population haplotype inference. Uncovering the haplotypes of single
nucleotide polymorphisms is essential for many biological and medical
applications. While it is uncommon for the genotype data to be pooled from
multiple ethnically distinct populations, few existing programs have explicitly
leveraged the individual ethnic information for haplotype inference. In this
paper we present a new haplotype inference program, Haploi, which makes use of
such information and is readily applicable to genotype sequences with thousands
of SNPs from heterogeneous populations, with competent and sometimes superior
speed and accuracy comparing to the state-of-the-art programs. Underlying
Haploi is a new haplotype distribution model based on a nonparametric Bayesian
formalism known as the hierarchical Dirichlet process, which represents a
tractable surrogate to the coalescent process. The proposed model is
exchangeable, unbounded, and capable of coupling demographic information of
different populations.Comment: Published in at http://dx.doi.org/10.1214/08-AOAS225 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org