Explore Research Products in the PAR
It may take a few hours for recently added research products to appear in PAR search results.


Title: SiPhyNetwork : An R package for simulating phylogenetic networks
Abstract Gene flow is increasingly recognized as an important macroevolutionary process. The many mechanisms that contribute to gene flow (e.g. introgression, hybridization, lateral gene transfer) uniquely affect the diversification of dynamics of species, making it important to be able to account for these idiosyncrasies when constructing phylogenetic models. Existing phylogenetic‐network simulators for macroevolution are limited in the ways they model gene flow.We presentSiPhyNetwork, an R package for simulating phylogenetic networks under a birth–death‐hybridization process.Our package unifies the existing birth–death‐hybridization models while also extending the toolkit for modelling gene flow. This tool can create patterns of reticulation such as hybridization, lateral gene transfer, and introgression.Specifically, we model different reticulate events by allowing events to either add, remove or keep constant the number of lineages. Additionally, we allow reticulation events to be trait dependent, creating the ability to model the expanse of isolating mechanisms that prevent gene flow. This tool makes it possible for researchers to model many of the complex biological factors associated with gene flow in a phylogenetic context.  more » « less
Award ID(s):
2144367
PAR ID:
10483912
Author(s) / Creator(s):
; ;
Publisher / Repository:
MEE
Date Published:
Journal Name:
Methods in Ecology and Evolution
Volume:
14
Issue:
7
ISSN:
2041-210X
Page Range / eLocation ID:
1687 to 1698
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ; ; ; ; ; ; ; (, Methods in Ecology and Evolution)
    Abstract ThePCMBase Rpackage is a powerful computational tool that enables efficient calculations of likelihoods for a wide range of phylogenetic Gaussian models.Taking advantage of it, we redesigned theRpackagemvSLOUCH.Here, we demonstrate how the new version of the package can be used to thoroughly examine the evolution and adaptation of traits in a large dataset of 1252 vascular plants through the use of multivariate Ornstein–Uhlenbeck processes.The results of our analysis demonstrate the ability of the modelling framework to distinguish between various alternative hypotheses regarding the evolution of functional traits in angiosperms. 
    more » « less
  2. ; ; ; ; ; (, Journal of Mathematical Biology)
    Abstract Phylogenetic networks can represent evolutionary events that cannot be described by phylogenetic trees. These networks are able to incorporate reticulate evolutionary events such as hybridization, introgression, and lateral gene transfer. Recently, network-based Markov models of DNA sequence evolution have been introduced along with model-based methods for reconstructing phylogenetic networks. For these methods to be consistent, the network parameter needs to be identifiable from data generated under the model. Here, we show that the semi-directed network parameter of a triangle-free, level-1 network model with any fixed number of reticulation vertices is generically identifiable under the Jukes–Cantor, Kimura 2-parameter, or Kimura 3-parameter constraints. 
    more » « less
  3. ; ; (, Methods in Ecology and Evolution)
    Abstract Collective motion, that is the coordinated spatial and temporal organisation of individuals, is a core element in the study of collective animal behaviour. The self‐organised properties of how a group moves influence its various behavioural and ecological processes, such as predator–prey dynamics, social foraging and migration. However, little is known about the inter‐ and intra‐specific variation in collective motion. Despite the significant advancement in high‐resolution tracking of multiple individuals within groups, providing collective motion data for animals in the laboratory and the field, a framework to perform quantitative comparisons across species and contexts is lacking.Here, we present theswaRmversepackage. Building on two existing R packages,trackdfandswaRm,swaRmverseenables the identification and analysis of collective motion ‘events’, as presented in Papadopoulou et al. (2023), creating a unit of comparison across datasets. We describe the package's structure and showcase its functionality using existing datasets from several species and simulated trajectories from an agent‐based model.From positional time‐series data for multiple individuals (x‐y‐t‐id),swaRmverseidentifies events of collective motion based on the distribution of polarisation and group speed. For each event, a suite of validated biologically meaningful metrics are calculated, and events are placed into a ‘swarm space’ through dimensional reduction techniques.Our package provides the first automated pipeline enabling the analysis of data on collective behaviour. The package allows the calculation and use of complex metrics for users without a strong quantitative background and will promote communication and data‐sharing across disciplines, standardising the quantification of collective motion across species and promoting comparative investigations. 
    more » « less
  4. ; ; ; ; ; ; ; ; ; ; et al (, Methods in Ecology and Evolution)
    Abstract Accurate quantification of soil carbon fluxes is essential to reduce uncertainty in estimates of the terrestrial carbon sink. However, these fluxes vary over time and across ecosystem types and so, it can be difficult to estimate them accurately across large scales. The flux‐gradient method estimates soil carbon fluxes using co‐located measurements of soil CO2concentration, soil temperature, soil moisture and other soil properties. The National Ecological Observatory Network (NEON) provides such data across 20 ecoclimatic domains spanning the continental U.S., Puerto Rico, Alaska and Hawai‘i.We present an R software package (neonSoilFlux) that acquires soil environmental data to compute half‐hourly soil carbon fluxes for each soil replicate plot at a given terrestrial NEON site. To assess the computed fluxes, we visited six focal NEON sites and measured soil carbon fluxes using a closed‐dynamic chamber approach.Outputs from theneonSoilFluxshowed agreement with measured fluxes (R2between measured andneonSoilFluxoutputs ranging from 0.12 to 0.77 depending on calculation method used); measured outputs generally fell within the range of calculated uncertainties from the gradient method. Calculated fluxes fromneonSoilFluxaggregated to the daily scale exhibited expected site‐specific seasonal patterns.While the flux‐gradient method is broadly effective, its accuracy is highly sensitive to site‐specific inputs, including the extent to which gap‐filing techniques are used to interpolate missing sensor data and to estimates of soil diffusivity and moisture content. Future refinement and validation ofneonSoilFluxoutputs can contribute to existing databases of soil carbon flux measurements, providing near real‐time estimates of a critical component of the terrestrial carbon cycle. 
    more » « less
  5. ; ; ; ; (, New Phytologist)
    Summary The genusDelphiniumexemplifies the complexity of plant diversification in mountainous regions, where rapid speciation, hybridization, and morphological convergence frequently obscure species boundaries. The North American lineageDelphiniumsect.Diedropetalahas rapidly radiated across a range of ecological habitats, from alpine tundra to desert grasslands, forming an iconic component of western wild flower communities.Here, we present a genome‐scale phylogeny of 34 taxa using ddRAD‐seq data from 150 individuals sampled across their geographic ranges.Our results reveal strong phylogenetic structure corresponding to biogeographic regions, including several well‐supported clades that cut across existing taxonomic subsections, emphasizing the need for taxonomic revision. Hybridization and introgression are widespread, occurring both within and between these regional clades. Most species are connected through a syngameon‐like network of introgression, with few widespread species acting as central hubs. We describe six higher‐level clade names and use an agent‐based artificial intelligence analysis to identify morphological synapomorphies that align with our genomic findings.Our study demonstrates that geography and gene flow have played a dominant role in shaping the evolutionary history ofDelphiniumin North America, offering a framework for revising its taxonomy and informing future conservation efforts. 
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Text Encoded Conversion
  • XML
  • Save / Share this Record
  • Send to Email