scholarly journals On the Variance of Internode Distance Under the Multispecies Coalescent

2018 ◽  
pp. 196-206
Author(s):  
Sébastien Roch
Keyword(s):  
Multispecies Coalescent ◽  
Internode Distance

scholarly journals Optimal data partitioning, multispecies coalescent and Bayesian concordance analyses resolve early divergences of the grape family (Vitaceae)

Cladistics ◽  
2017 ◽  
Vol 34 (1) ◽  
pp. 57-77 ◽  
Author(s):  
Limin Lu ◽  
Cymon J. Cox ◽  
Sarah Mathews ◽  
Wei Wang ◽  
Jun Wen ◽  
...  
Keyword(s):  
Data Partitioning ◽  
Multispecies Coalescent

scholarly journals Internode Distance-Based Redundancy Reliable Transport in Underwater Sensor Networks

2010 ◽  
Vol 2010 (1) ◽  
Author(s):  
Bin Liu ◽  
Hongyang Chen ◽  
Xianfu Lei ◽  
Fengyuan Ren ◽  
Kaoru Sezaki
Keyword(s):  
Sensor Networks ◽  
Underwater Sensor Networks ◽  
Internode Distance ◽  
Reliable Transport

scholarly journals Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics

2016 ◽  
Vol 94 ◽  
pp. 447-462 ◽  
Author(s):  
Scott V. Edwards ◽  
Zhenxiang Xi ◽  
Axel Janke ◽  
Brant C. Faircloth ◽  
John E. McCormack ◽  
...  
Keyword(s):  
Coalescent Model ◽  
Multispecies Coalescent

scholarly journals Phylogeny and character evolution in the Dacrymycetes, and systematics of Unilacrymaceae and Dacryonaemataceae fam. nov.

2020 ◽  
Vol 44 (1) ◽  
pp. 161-205
Author(s):  
J.C. Zamora ◽  
S. Ekman
Keyword(s):  
Species Level ◽  
Single Locus ◽  
Phenotypic Characters ◽  
New Family ◽  
Multispecies Coalescent ◽  
Morphometric Analyses ◽  
Methodological Approaches ◽  
First Time ◽  
A New Species ◽  
Multilocus Phylogeny

We present a multilocus phylogeny of the class Dacrymycetes, based on data from the 18S, ITS, 28S, RPB1, RPB2, TEF-1α, 12S, and ATP6 DNA regions, with c. 90 species including the types of most currently accepted genera. A variety of methodological approaches was used to infer phylogenetic relationships among the Dacrymycetes, from a supermatrix strategy using maximum likelihood and Bayesian inference on a concatenated dataset, to coalescence-based calculations, such as quartet-based summary methods of independent single-locus trees, and Bayesian integration of single-locus trees into a species tree under the multispecies coalescent. We evaluate for the first time the taxonomic usefulness of some cytological phenotypic characters, i.e., vacuolar contents (vacuolar bodies and lipid bodies), number of nuclei of recently discharged basidiospores, and pigments, with especial emphasis on carotenoids. These characters, along with several others traditionally used for the taxonomy of this group (basidium shape, presence and morphology of clamp connections, morphology of the terminal cells of cortical/marginal hyphae, presence and degree of ramification of the hyphidia), are mapped on the resulting phylogenies and their evolution through the class Dacrymycetes discussed. Our analyses reveal five lineages that putatively represent five different families, four of which are accepted and named. Three out of these four lineages correspond to previously circumscribed and published families (Cerinomycetaceae, Dacrymycetaceae, and Unilacrymaceae), and one is proposed as the new family Dacryonaemataceae. Provisionally, only a single order, Dacrymycetales, is accepted with in the class. Furthermore, the systematics of the two smallest families, Dacryonaemataceae and Unilacrymaceae, are investigated to the species level, using coalescence-based species delimitation on multilocus DNA data, and a detailed morphological study including morphometric analyses of the basidiospores. Three species are accepted in Dacryonaema, the type, Da. rufum, the newly combined Da. macnabbii (basionym Dacrymyces macnabbii), and a new species named Da. macrosporum. Two species are accepted in Unilacryma, the new U. bispora, and the type, U. unispora, the latter treated in a broad sense pending improved sampling across the Holarctic.

scholarly journals Impact of Ghost Introgression on Coalescent-based Species Tree Inference and Estimation of Divergence Time

2022 ◽  
Author(s):  
XiaoXu Pang ◽  
Da-Yong Zhang
Keyword(s):  
Incomplete Lineage Sorting ◽  
Divergence Time ◽  
Species Tree ◽  
Gene Trees ◽  
Species Trees ◽  
Lineage Sorting ◽  
Multispecies Coalescent ◽  
Tree Inference ◽  
Tree Methods ◽  
The Impact

The species studied in any evolutionary investigation generally constitute a very small proportion of all the species currently existing or that have gone extinct. It is therefore likely that introgression, which is widespread across the tree of life, involves "ghosts," i.e., unsampled, unknown, or extinct lineages. However, the impact of ghost introgression on estimations of species trees has been rarely studied and is thus poorly understood. In this study, we use mathematical analysis and simulations to examine the robustness of species tree methods based on a multispecies coalescent model under gene flow sourcing from an extant or ghost lineage. We found that very low levels of extant or ghost introgression can result in anomalous gene trees (AGTs) on three-taxon rooted trees if accompanied by strong incomplete lineage sorting (ILS). In contrast, even massive introgression, with more than half of the recipient genome descending from the donor lineage, may not necessarily lead to AGTs. In cases involving an ingroup lineage (defined as one that diverged no earlier than the most basal species under investigation) acting as the donor of introgression, the time of root divergence among the investigated species was either underestimated or remained unaffected, but for the cases of outgroup ghost lineages acting as donors, the divergence time was generally overestimated. Under many conditions of ingroup introgression, the stronger the ILS was, the higher was the accuracy of estimating the time of root divergence, although the topology of the species tree is more prone to be biased by the effect of introgression.

scholarly journals Morphological Characterization of Mulberry (Morus spp.) Accessions Grown in Kenya

2013 ◽  
Vol 3 (1) ◽  
pp. 10 ◽  
Author(s):  
Nderitu Wangari Peris ◽  
Kinyua Mirriam Gacheri ◽  
Mutui Mwendwa Theophillus ◽  
Ngode Lucas
Keyword(s):  
Hierarchical Cluster ◽  
Morphological Characterization ◽  
Phenotypic Traits ◽  
Mulberry Leaf ◽  
Leaf Yield ◽  
Morus Spp ◽  
Positive Correlations ◽  
Internode Distance ◽  
Number Of Branches

<p>Genetic divergence of five mulberry accessions including Embu, Thika, Thailand (<em>M. alba</em>), Kanva-2 and S41 (<em>M. indica</em>) grown in Kenya were examined using twelve phenotypic traits. The assessment of phenotypic traits was done in a field study in two localities, Nairobi and Eldoret. The traits that were significantly different across the mulberry accessions included lamina width and petiole length (P ? 0.01), petiole width and growth height (P ? 0.05), internodes distance and number of branches (P ? 0.001). The Duncan’s Multiple Range Test (DMRT) results were used to generate a dendrogram derived from hierarchical cluster analysis that further partitioned the mulberry accessions into four groups. Embu and Thailand accessions grouped together while S41, Thika and Kanva-2 accessions grouped separately. Embu and Thailand accessions were characterized by fewer numbers of branches than the rest of the accessions. Thika accession had high number of branches and short internode distance. Significant and positive correlations were found between leaf yield traits except in internode distance and number of branches which were significant and negatively correlated. Significant and positive correlations can be utilized since they are rewarding for mulberry leaf yield improvement.</p>

scholarly journals MSCquartets 1.0: Quartet methods for species trees and networks under the multispecies coalescent model in R

2020 ◽  
Author(s):  
John A Rhodes ◽  
Hector Baños ◽  
Jonathan D Mitchell ◽  
Elizabeth S Allman
Keyword(s):  
Network Inference ◽  
Incomplete Lineage Sorting ◽  
R Package ◽  
Species Tree ◽  
Supplementary Information ◽  
Species Trees ◽  
Lineage Sorting ◽  
Coalescent Model ◽  
Multispecies Coalescent ◽  
Tree Inference

Abstract Summary MSCquartets is an R package for species tree hypothesis testing, inference of species trees, and inference of species networks under the Multispecies Coalescent model of incomplete lineage sorting and its network analog. Input for these analyses are collections of metric or topological locus trees which are then summarized by the quartets displayed on them. Results of hypothesis tests at user-supplied levels are displayed in a simplex plot by color-coded points. The package implements the QDC and WQDC algorithms for topological and metric species tree inference, and the NANUQ algorithm for level-1 topological species network inference, all of which give statistically consistent estimators under the model. Availability MSCquartets is available through the Comprehensive R Archive Network: https://CRAN.R-project.org/package=MSCquartets. Supplementary information Supplementary materials, including example data and analyses, are incorporated into the package.

scholarly journals Detecting destabilizing species in the phylogenetic backbone of Potentilla (Rosaceae) using low-copy nuclear markers

AoB Plants ◽  
2020 ◽  
Vol 12 (3) ◽  
Author(s):  
Nannie L Persson ◽  
Ingrid Toresen ◽  
Heidi Lie Andersen ◽  
Jenny E E Smedmark ◽  
Torsten Eriksson
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Data Sets ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Nuclear Markers ◽  
Data Set ◽  
Multispecies Coalescent ◽  
Single Marker ◽  
Named Groups

Abstract The genus Potentilla (Rosaceae) has been subjected to several phylogenetic studies, but resolving its evolutionary history has proven challenging. Previous analyses recovered six, informally named, groups: the Argentea, Ivesioid, Fragarioides, Reptans, Alba and Anserina clades, but the relationships among some of these clades differ between data sets. The Reptans clade, which includes the type species of Potentilla, has been noticed to shift position between plastid and nuclear ribosomal data sets. We studied this incongruence by analysing four low-copy nuclear markers, in addition to chloroplast and nuclear ribosomal data, with a set of Bayesian phylogenetic and Multispecies Coalescent (MSC) analyses. A selective taxon removal strategy demonstrated that the included representatives from the Fragarioides clade, P. dickinsii and P. fragarioides, were the main sources of the instability seen in the trees. The Fragarioides species showed different relationships in each gene tree, and were only supported as a monophyletic group in a single marker when the Reptans clade was excluded from the analysis. The incongruences could not be explained by allopolyploidy, but rather by homoploid hybridization, incomplete lineage sorting or taxon sampling effects. When P. dickinsii and P. fragarioides were removed from the data set, a fully resolved, supported backbone phylogeny of Potentilla was obtained in the MSC analysis. Additionally, indications of autopolyploid origins of the Reptans and Ivesioid clades were discovered in the low-copy gene trees.

scholarly journals Cryptic diversity in Brazilian endemic monkey frogs (Hylidae, Phyllomedusinae, Pithecopus) revealed by multispecies coalescent and integrative approaches

2019 ◽  
Vol 132 ◽  
pp. 105-116 ◽  
Author(s):  
Elisa Karen Silva Ramos ◽  
Rafael Félix de Magalhães ◽  
Núbia Carla Santos Marques ◽  
Délio Baêta ◽  
Paulo Christiano Anchietta Garcia ◽  
...  
Keyword(s):  
Cryptic Diversity ◽  
Multispecies Coalescent
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