19,406 research outputs found
Bayesian co-estimation of selfing rate and locus-specific mutation rates for a partially selfing population
We present a Bayesian method for characterizing the mating system of
populations reproducing through a mixture of self-fertilization and random
outcrossing. Our method uses patterns of genetic variation across the genome as
a basis for inference about pure hermaphroditism, androdioecy, and gynodioecy.
We extend the standard coalescence model to accommodate these mating systems,
accounting explicitly for multilocus identity disequilibrium, inbreeding
depression, and variation in fertility among mating types. We incorporate the
Ewens Sampling Formula (ESF) under the infinite-alleles model of mutation to
obtain a novel expression for the likelihood of mating system parameters. Our
Markov chain Monte Carlo (MCMC) algorithm assigns locus-specific mutation
rates, drawn from a common mutation rate distribution that is itself estimated
from the data using a Dirichlet Process Prior (DPP) model. Among the parameters
jointly inferred are the population-wide rate of self-fertilization,
locus-specific mutation rates, and the number of generations since the most
recent outcrossing event for each sampled individual
An Empirical Calibration of the Completeness of the SDSS Quasar Survey
Spectra of nearly 20000 point-like objects to a Galactic reddening corrected
magnitude of i=19.1 have been obtained to test the completeness of the SDSS
quasar survey. The spatially-unresolved objects were selected from all regions
of color space, sparsely sampled from within a 278 sq. deg. area of sky covered
by this study. Only ten quasars were identified that were not targeted as
candidates by the SDSS quasar survey (including both color and radio source
selection). The inferred density of unresolved quasars on the sky that are
missed by the SDSS algorithm is 0.44 per sq. deg, compared to 8.28 per sq. deg.
for the selected quasar density, giving a completeness of 94.9(+2.6,-3.8) to
the limiting magnitude. Omitting radio selection reduces the color-only
selection completeness by about 1%. Of the ten newly identified quasars, three
have detected broad absorption line systems, six are significantly redder than
other quasars at the same redshift, and four have redshifts between 2.7 and 3.0
(the redshift range where the SDSS colors of quasars intersect the stellar
locus). The fraction of quasars missed due to image defects and blends is
approximately 4%, but this number varies by a few percent with magnitude.
Quasars with extended images comprise about 6% of the SDSS sample, and the
completeness of the selection algorithm for extended quasars is approximately
81%, based on the SDSS galaxy survey. The combined end-to-end completeness for
the SDSS quasar survey is approximately 89%. The total corrected density of
quasars on the sky to i=19.1 is estimated to be 10.2 per sq. deg.Comment: 37 pages, 10 figures, accepted for publication in A
Inference of Ancestral Recombination Graphs through Topological Data Analysis
The recent explosion of genomic data has underscored the need for
interpretable and comprehensive analyses that can capture complex phylogenetic
relationships within and across species. Recombination, reassortment and
horizontal gene transfer constitute examples of pervasive biological phenomena
that cannot be captured by tree-like representations. Starting from hundreds of
genomes, we are interested in the reconstruction of potential evolutionary
histories leading to the observed data. Ancestral recombination graphs
represent potential histories that explicitly accommodate recombination and
mutation events across orthologous genomes. However, they are computationally
costly to reconstruct, usually being infeasible for more than few tens of
genomes. Recently, Topological Data Analysis (TDA) methods have been proposed
as robust and scalable methods that can capture the genetic scale and frequency
of recombination. We build upon previous TDA developments for detecting and
quantifying recombination, and present a novel framework that can be applied to
hundreds of genomes and can be interpreted in terms of minimal histories of
mutation and recombination events, quantifying the scales and identifying the
genomic locations of recombinations. We implement this framework in a software
package, called TARGet, and apply it to several examples, including small
migration between different populations, human recombination, and horizontal
evolution in finches inhabiting the Gal\'apagos Islands.Comment: 33 pages, 12 figures. The accompanying software, instructions and
example files used in the manuscript can be obtained from
https://github.com/RabadanLab/TARGe
Natural hybridization between Populus nigra L. and P. x canadensis Moench. Hybrid offspring competes for niches along the Rhine river in the Netherlands
Black poplar (Populus nigra L.) is a major species for European riparian forests but its abundance has decreased over the decades due to human influences. For restoration of floodplain woodlands, the remaining black poplar stands may act as source population. A potential problem is that P. nigra and Populus deltoides have contributed to many interspecific hybrids, which have been planted in large numbers. As these Populus x canadensis clones have the possibility to intercross with wild P. nigra trees, their offspring could establish themselves along European rivers. In this study, we have sampled 44 poplar seedlings and young trees that occurred spontaneously along the Rhine river and its tributaries in the Netherlands. Along these rivers, only a few native P. nigra L. populations exist in combination with many planted cultivated P. x canadensis trees. By comparison to reference material from P. nigra, P. deltoides and P. x canadensis, species-specific AFLP bands and microsatellite alleles indicated that nearly half of the sampled trees were not pure P. nigra but progeny of natural hybridisation that had colonised the Rhine river banks. The posterior probability method as implemented in NewHybrids using microsatellite data was the superior method in establishing the most likely parentage. The results of this study indicate that offspring of hybrid cultivated poplars compete for the same ecological niche as native black poplars
An Improved Approximate-Bayesian Model-choice Method for Estimating Shared Evolutionary History
To understand biological diversification, it is important to account for
large-scale processes that affect the evolutionary history of groups of
co-distributed populations of organisms. Such events predict temporally
clustered divergences times, a pattern that can be estimated using genetic data
from co-distributed species. I introduce a new approximate-Bayesian method for
comparative phylogeographical model-choice that estimates the temporal
distribution of divergences across taxa from multi-locus DNA sequence data. The
model is an extension of that implemented in msBayes. By reparameterizing the
model, introducing more flexible priors on demographic and divergence-time
parameters, and implementing a non-parametric Dirichlet-process prior over
divergence models, I improved the robustness, accuracy, and power of the method
for estimating shared evolutionary history across taxa. The results demonstrate
the improved performance of the new method is due to (1) more appropriate
priors on divergence-time and demographic parameters that avoid prohibitively
small marginal likelihoods for models with more divergence events, and (2) the
Dirichlet-process providing a flexible prior on divergence histories that does
not strongly disfavor models with intermediate numbers of divergence events.
The new method yields more robust estimates of posterior uncertainty, and thus
greatly reduces the tendency to incorrectly estimate models of shared
evolutionary history with strong support.Comment: 48 pages, 8 figures, 4 tables, 35 pages of supporting information
with 1 supporting table and 33 supporting figure
Bovine polledness
The persistent horns are an important trait of speciation for the family Bovidae with complex morphogenesis taking place briefly after birth. The polledness is highly favourable in modern cattle breeding systems but serious animal welfare issues urge for a solution in the production of hornless cattle other than dehorning. Although the dominant inhibition of horn morphogenesis was discovered more than 70 years ago, and the causative mutation was mapped almost 20 years ago, its molecular nature remained unknown. Here, we report allelic heterogeneity of the POLLED locus. First, we mapped the POLLED locus to a âź381-kb interval in a multi-breed case-control design. Targeted re-sequencing of an enlarged candidate interval (547 kb) in 16 sires with known POLLED genotype did not detect a common allele associated with polled status. In eight sires of Alpine and Scottish origin (four polled versus four horned), we identified a single candidate mutation, a complex 202 bp insertion-deletion event that showed perfect association to the polled phenotype in various European cattle breeds, except Holstein-Friesian. The analysis of the same candidate interval in eight Holsteins identified five candidate variants which segregate as a 260 kb haplotype also perfectly associated with the POLLED gene without recombination or interference with the 202 bp insertion-deletion. We further identified bulls which are progeny tested as homozygous polled but bearing both, 202 bp insertion-deletion and Friesian haplotype. The distribution of genotypes of the two putative POLLED alleles in large semi-random sample (1,261 animals) supports the hypothesis of two independent mutations
Genetic differentiation in Scottish populations of the pine beauty moth Panolis flammea (Lepidoptera: Noctuidae)
Pine beauty moth, Panolis flammea (Denis & SchiffermĂźller), is a recent but persistent pest of lodgepole pine plantations in Scotland, but exists naturally at low levels within remnants and plantations of Scots pine. To test whether separate host races occur in lodgepole and Scots pine stands and to examine colonization dynamics, allozyme, randomly amplified polymorphic DNA (RAPD) and mitochondrial variation were screened within a range of Scottish samples. RAPD analysis indicated limited long distance dispersal (FST = 0.099), and significant isolation by distance (P < 0.05); but that colonization between more proximate populations was often variable, from extensive to limited exchange. When compared with material from Germany, Scottish samples were found to be more diverse and significantly differentiated for all markers. For mtDNA, two highly divergent groups of haplotypes were evident, one group contained both German and Scottish samples and the other was predominantly Scottish. No genetic differentiation was evident between P. flammea populations sampled from different hosts, and no diversity bottleneck was observed in the lodgepole group. Indeed, lodgepole stands appear to have been colonized on multiple occasions from Scots pine sources and neighbouring populations on different hosts are close to panmixia.A.J. Lowe, B.J. Hicks, K. Worley, R.A. Ennos, J.D. Morman, G. Stone and A.D. Wat
Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting
Phylogenetic networks are necessary to represent the tree of life expanded by
edges to represent events such as horizontal gene transfers, hybridizations or
gene flow. Not all species follow the paradigm of vertical inheritance of their
genetic material. While a great deal of research has flourished into the
inference of phylogenetic trees, statistical methods to infer phylogenetic
networks are still limited and under development. The main disadvantage of
existing methods is a lack of scalability. Here, we present a statistical
method to infer phylogenetic networks from multi-locus genetic data in a
pseudolikelihood framework. Our model accounts for incomplete lineage sorting
through the coalescent model, and for horizontal inheritance of genes through
reticulation nodes in the network. Computation of the pseudolikelihood is fast
and simple, and it avoids the burdensome calculation of the full likelihood
which can be intractable with many species. Moreover, estimation at the
quartet-level has the added computational benefit that it is easily
parallelizable. Simulation studies comparing our method to a full likelihood
approach show that our pseudolikelihood approach is much faster without
compromising accuracy. We applied our method to reconstruct the evolutionary
relationships among swordtails and platyfishes (: Poeciliidae),
which is characterized by widespread hybridizations
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