1,704 research outputs found
Bayesian Species Delimitation Can Be Robust to Guide-Tree Inference Errors
distribution, and reproduction in any medium, provided the original work is properly cited
Molecular phylogenetics: principles and practice
Phylogenies are important for addressing various biological questions such as relationships among species or genes, the origin and spread of viral infection and the demographic changes and migration patterns of species. The advancement of sequencing technologies has taken phylogenetic analysis to a new height. Phylogenies have permeated nearly every branch of biology, and the plethora of phylogenetic methods and software packages that are now available may seem daunting to an experimental biologist. Here, we review the major methods of phylogenetic analysis, including parsimony, distance, likelihood and Bayesian methods. We discuss their strengths and weaknesses and provide guidance for their use
Unguided Species Delimitation Using DNA Sequence Data from Multiple Loci
A method was developed for simultaneous Bayesian inference of species delimitation and species phylogeny using the multispecies coalescent model. The method eliminates the need for a user-specified guide tree in species delimitation and incorporates phylogenetic uncertainty in a Bayesian framework. The nearest-neighbor interchange algorithm was adapted to propose changes to the species tree, with the gene trees for multiple loci altered in the proposal to avoid conflicts with the newly proposed species tree. We also modify our previous scheme for specifying priors for species delimitation models to construct joint priors for models of species delimitation and species phylogeny. As in our earlier method, the modified algorithm integrates over gene trees, taking account of the uncertainty of gene tree topology and branch lengths given the sequence data. We conducted a simulation study to examine the statistical properties of the method using six populations (two sequences each) and a true number of three species, with values of divergence times and ancestral population sizes that are realistic for recently diverged species. The results suggest that the method tends to be conservative with high posterior probabilities being a confident indicator of species status. Simulation results also indicate that the power of the method to delimit species increases with an increase of the divergence times in the species tree, and with an increased number of gene loci. Reanalyses of two data sets of cavefish and coast horned lizards suggest considerable phylogenetic uncertainty even though the data are informative about species delimitation. We discuss the impact of the prior on models of species delimitation and species phylogeny and of the prior on population size parameters (θ) on Bayesian species delimitation
Efficient Bayesian species tree inference under the multispecies coalescent
We develop a Bayesian method for inferring the species phylogeny under the multispecies coalescent (MSC)
model. To improve the mixing properties of the Markov chain Monte Carlo (MCMC) algorithm that traverses
the space of species trees, we implement two efficient MCMC proposals: the first is based on the
Subtree Pruning and Regrafting (SPR) algorithm and the second is based on a node-slider algorithm. Like
the Nearest-Neighbor Interchange (NNI) algorithm we implemented previously, both new algorithms propose
changes to the species tree while simultaneously altering the gene trees at multiple genetic loci to automatically
avoid conflicts with the newly proposed species tree. The method integrates over gene trees, naturally
taking account of the uncertainty of gene tree topology and branch lengths given the sequence data. A simulation
study was performed to examine the statistical properties of the new method. The method was found
to show excellent statistical performance, inferring the correct species tree with near certainty when 10 loci
were included in the dataset. The prior on species trees has some impact, particularly for small numbers
of loci. We analyzed several previously published datasets (both real and simulated) for rattlesnakes and
Philippine shrews, in comparison with alternative methods. The results suggest that the Bayesian coalescentbased
method is statistically more efficient than heuristic methods based on summary statistics, and that our
implementation is computationally more efficient than alternative full-likelihood methods under the MSC.
Parameter estimates for the rattlesnake data suggest drastically different evolutionary dynamics between the
nuclear and mitochondrial loci, even though they support largely consistent species trees. We discuss the different
challenges facing the marginal likelihood calculation and transmodel MCMC as alternative strategies
for estimating posterior probabilities for species trees
Molecular clock dating
This chapter reviews the history of the molecular clock,
its impact on molecular evolution, and the controversies
surrounding mechanisms of evolutionary rate variation
and the application of the clock to date species divergences.
We review current molecular clock dating methods,
including maximum likelihood and Bayesian methods,
with an emphasis on relaxing the clock and on
incorporating uncertainties into fossil calibrations
Noorsootöötajate vaatepunkt: kuidas toetada noorte osalust?
Youth workers' views: how to support youth participation?AbstractThe article aims to understand how and why youth workers act as supporters of youth participation. The article is based on the analysis of focus group interviews with 15 Estonian experts in the youth field. Numerous previous studies have emphasized the multifaceted construction of participation and the possibility of coexistence of traditional and new forms of participation - and the values and challenges of youth work in supporting and making sense of youth participation. This study shows how Estonian youth workers understand youth participation, their role in supporting the participation, and the challenges youth workers see in the general process of youth participation. Youth workers consider the support of the participation of young people as an essential part of their work. They see themselves as encouragers, motivators, information givers and awareness raisers, mentors, and allies in making the voice of young people heard more clearly in society. Youth participation is primarily concidered as the right and opportunity to shape and influence decisions that concern young people´s lives. Supporting youth participation is perceived as a long-term process that should be based on the needs and interests of young people. As an obstacle, the informants pointed out that the social readiness or agreement to listen to young people, understand and consider the opinion of young people is insufficient and ‘fake engagement’ reduces the enthusiasm of young people
Recommended from our members
Early detection of highly transmissible viral variants using phylogenomics
As demonstrated by the SARS-CoV-2 pandemic, the emergence of novel viral strains with increased transmission rates poses a serious threat to global health. Statistical models of genome sequence evolution may provide a critical tool for early detection of these strains. Using a novel stochastic model that links transmission rates to the entire viral genome sequence, we study the utility of phylogenetic methods that use a phylogenetic tree relating viral samples versus count-based methods that use case counts of variants over time exclusively to detect increased transmission rates and identify candidate causative mutations. We find that phylogenies in particular can detect novel transmission-enhancing variants very soon after their origin and may facilitate the development of early detection systems for outbreak surveillance
Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation
The use of fossil evidence to calibrate divergence time estimation has a long
history. More recently Bayesian MCMC has become the dominant method of
divergence time estimation and fossil evidence has been re-interpreted as the
specification of prior distributions on the divergence times of calibration
nodes. These so-called "soft calibrations" have become widely used but the
statistical properties of calibrated tree priors in a Bayesian setting has not
been carefully investigated. Here we clarify that calibration densities, such
as those defined in BEAST 1.5, do not represent the marginal prior distribution
of the calibration node. We illustrate this with a number of analytical results
on small trees. We also describe an alternative construction for a calibrated
Yule prior on trees that allows direct specification of the marginal prior
distribution of the calibrated divergence time, with or without the restriction
of monophyly. This method requires the computation of the Yule prior
conditional on the height of the divergence being calibrated. Unfortunately, a
practical solution for multiple calibrations remains elusive. Our results
suggest that direct estimation of the prior induced by specifying multiple
calibration densities should be a prerequisite of any divergence time dating
analysis
The Influence of Gene Flow on Species Tree Estimation: A Simulation Study
Gene flow among populations or species and incomplete lineage sorting (ILS) are two evolutionary processes
responsible for generating gene tree discordance and therefore hindering species tree estimation. Numerous studies have evaluated the impacts of ILS on species tree inference, yet the ramifications of gene flow on species trees remain less studied. Here, we simulate and analyse multilocus sequence data generated with ILS and gene flow to quantify their impacts on species tree inference. We characterize species tree estimation errors under various models of gene flow, such as the isolation-migration model, the n-island model, and gene flow between non-sister species or involving ancestral species, and species boundaries crossed by a single gene copy (allelic introgression) or by a single migrant individual. These
patterns of gene flow are explored on species trees of different sizes (4 vs. 10 species), at different time scales (shallow vs. deep), and with different migration rates. Species trees are estimated with the multispecies coalescent model using Bayesian methods (BEST and *BEAST) and with a summary statistic approach (MPEST) that facilitates phylogenomic-scale analysis. Even in cases where the topology of the species tree is estimated with high accuracy, we find that gene flow can result in overestimates of population sizes (species tree dilation) and underestimates of species divergence times (species
tree compression). Signatures of migration events remain present in the distribution of coalescent times for gene trees, and with sufficient data it is possible to identify those loci that have crossed species boundaries. These results highlight the need for careful sampling design in phylogeographic and species delimitation studies as gene flow, introgression, or incorrect sample assignments can bias the estimation of the species tree topology and of parameter estimates such as
population sizes and divergence times
- …