scholarly journals Phylogenetic informativeness analyses to clarify past diversification processes in Cucurbitaceae

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Sidonie Bellot ◽  
Thomas C. Mitchell ◽  
Hanno Schaefer
Keyword(s):  
Phylogenetic Informativeness

scholarly journals Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes

2015 ◽  
Vol 92 ◽  
pp. 140-146 ◽  
Author(s):  
Princess S. Gilbert ◽  
Jonathan Chang ◽  
Calvin Pan ◽  
Eric M. Sobel ◽  
Janet S. Sinsheimer ◽  
...  
Keyword(s):  
Gene Markers ◽  
Ultraconserved Elements ◽  
Genome Wide ◽  
Phylogenetic Informativeness

scholarly journals A time and a place for everything: phylogenetic history and geography as joint predictors of oak plastome phylogeny

Genome ◽  
2017 ◽  
Vol 60 (9) ◽  
pp. 720-732 ◽  
Author(s):  
Kasey K. Pham ◽  
Andrew L. Hipp ◽  
Paul S. Manos ◽  
Richard C. Cronn
Keyword(s):  
Dna Sequences ◽  
North American ◽  
Introgressive Hybridization ◽  
White Oak ◽  
Gene Migration ◽  
The North ◽  
Geographic Structure ◽  
Phylogenetic Studies ◽  
Phylogenetic Informativeness ◽  
Lineage Divergence

Owing to high rates of introgressive hybridization, the plastid genome is poorly suited to fine-scale DNA barcoding and phylogenetic studies of the oak genus (Quercus, Fagaceae). At the tips of the oak plastome phylogeny, recent gene migration and reticulation generally cause topology to reflect geographic structure, while deeper branches reflect lineage divergence. In this study, we quantify the simple and partial effects of geographic proximity and nucleome-inferred phylogenetic history on oak plastome phylogeny at different evolutionary scales. Our study compares pairwise phylogenetic distances based on complete plastome sequences, pairwise phylogenetic distances from nuclear restriction site-associated DNA sequences (RADseq), and pairwise geographic distances for 34 individuals of the white oak clade representing 24 North American and Eurasian species. Within the North American white oak clade alone, phylogenetic history has essentially no effect on plastome variation, while geography explains 11%–21% of plastome phylogenetic variance. However, across multiple continents and clades, phylogeny predicts 30%–41% of plastome variation, geography 3%–41%. Tipwise attenuation of phylogenetic informativeness in the plastome means that in practical terms, plastome data has little use in solving phylogenetic questions, but can still be a useful barcoding or phylogenetic marker for resolving questions among major clades.

scholarly journals Evaluating Phylogenetic Informativeness as a Predictor of Phylogenetic Signal for Metazoan, Fungal, and Mammalian Phylogenomic Data Sets

2013 ◽  
Vol 2013 ◽  
pp. 1-14 ◽  
Author(s):  
Francesc López-Giráldez ◽  
Andrew H. Moeller ◽  
Jeffrey P. Townsend
Keyword(s):  
Phylogenetic Signal ◽  
Simulated Data ◽  
Quantitative Measure ◽  
Data Sets ◽  
Phylogenetic Informativeness ◽  
Phylogenetic Resolution ◽  
Taxonomic Groups ◽  
Diverse Groups ◽  
Simulated Data Sets ◽  
Selection Of

Phylogenetic research is often stymied by selection of a marker that leads to poor phylogenetic resolution despite considerable cost and effort. Profiles of phylogenetic informativeness provide a quantitative measure for prioritizing gene sampling to resolve branching order in a particular epoch. To evaluate the utility of these profiles, we analyzed phylogenomic data sets from metazoans, fungi, and mammals, thus encompassing diverse time scales and taxonomic groups. We also evaluated the utility of profiles created based on simulated data sets. We found that genes selected via their informativeness dramatically outperformed haphazard sampling of markers. Furthermore, our analyses demonstrate that the original phylogenetic informativeness method can be extended to trees with more than four taxa. Thus, although the method currently predicts phylogenetic signal without specifically accounting for the misleading effects of stochastic noise, it is robust to the effects of homoplasy. The phylogenetic informativeness rankings obtained will allow other researchers to select advantageous genes for future studies within these clades, maximizing return on effort and investment. Genes identified might also yield efficient experimental designs for phylogenetic inference for many sister clades and outgroup taxa that are closely related to the diverse groups of organisms analyzed.

scholarly journals Phylogenetic informativeness reconciles ray-finned fish molecular divergence times

2014 ◽  
Vol 14 (1) ◽  
Author(s):  
Alex Dornburg ◽  
Jeffrey P Townsend ◽  
Matt Friedman ◽  
Thomas J Near
Keyword(s):  
Divergence Times ◽  
Phylogenetic Informativeness ◽  
Molecular Divergence

scholarly journals Hundreds of nuclear and plastid loci yield insights into orchid relationships

2020 ◽  
Author(s):  
Oscar Alejandro Pérez-Escobar ◽  
Steven Dodsworth ◽  
Diego Bogarín ◽  
Sidonie Bellot ◽  
Juan A. Balbuena ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Nuclear Genome ◽  
Nuclear Gene ◽  
Gene Trees ◽  
Deep Time ◽  
Plastid Genomes ◽  
Phylogenetic Informativeness ◽  
History Of ◽  
Phylogenetic Framework

ABSTRACTPremise of the studyEvolutionary relationships in the species-rich Orchidaceae have historically relied on organellar DNA sequences and limited taxon sampling. Previous studies provided a robust plastid-maternal phylogenetic framework, from which multiple hypotheses on the drivers of orchid diversification have been derived. However, the extent to which the maternal evolutionary history of orchids is congruent with that of the nuclear genome has remained uninvestigated.MethodsWe inferred phylogenetic relationships from 294 low-copy nuclear genes sequenced/obtained using the Angiosperms353 universal probe set from 75 species representing 69 genera, 16 tribes and 24 subtribes. To test for topological incongruence between nuclear and plastid genomes, we constructed a tree from 78 plastid genes, representing 117 genera, 18 tribes and 28 subtribes and compared them using a co-phylogenetic approach. The phylogenetic informativeness and support of the Angiosperms353 loci were compared with those of the 78 plastid genes.Key ResultsPhylogenetic inferences of nuclear datasets produced highly congruent and robustly supported orchid relationships. Comparisons of nuclear gene trees and plastid gene trees using the latest co-phylogenetic tools revealed strongly supported phylogenetic incongruence in both shallow and deep time. Phylogenetic informativeness analyses showed that the Angiosperms353 genes were in general more informative than most plastid genes.ConclusionsOur study provides the first robust nuclear phylogenomic framework for Orchidaceae plus an assessment of intragenomic nuclear discordance, plastid-nuclear tree incongruence, and phylogenetic informativeness across the family. Our results also demonstrate what has long been known but rarely documented: nuclear and plastid phylogenetic trees are not fully congruent and therefore should not be considered interchangeable.

scholarly journals High Phylogenetic Utility of an Ultraconserved Element Probe Set Designed for Arachnida

2016 ◽  
Author(s):  
James Starrett ◽  
Shahan Derkarabetian ◽  
Marshal Hedin ◽  
Robert W. Bryson ◽  
John E. McCormack ◽  
...  
Keyword(s):  
Morphological Characters ◽  
Tree Of Life ◽  
Animal Group ◽  
Species Discovery ◽  
Population Genomic ◽  
Phylogenetic Informativeness ◽  
Genomic Studies ◽  
Genomic Regions ◽  
Probe Set ◽  
Conserved Genomic Regions

AbstractArachnida is an ancient, diverse, and ecologically important animal group that contains a number of species of interest for medical, agricultural, and engineering applications. Despite this applied importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to arachnid biology. Biologists have made considerable efforts to resolve the arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth of genetic resources, have confounded these attempts. Here, we present a genomic toolkit for arachnids featuring hundreds of conserved DNA regions (ultraconserved elements or UCEs) that allow targeted sequencing of any species in the arachnid tree of life. We used recently developed capture probes designed from conserved genomic regions of available arachnid genomes to enrich a sample of loci from 32 diverse arachnids. Sequence capture returned an average of 487 UCE loci for all species, with a range from 170 to 722. Phylogenetic analysis of these UCEs produced a highly resolved arachnid tree with relationships largely consistent with recent transcriptome-based phylogenies. We also tested the phylogenetic informativeness of UCE probes within the spider, scorpion, and harvestman orders, demonstrating the utility of these markers at shallower taxonomic scales, even down to the level of species differences. This probe set will open the door to phylogenomic and population genomic studies across the arachnid tree of life, enabling systematics, species delimitation, species discovery, and conservation of these diverse arthropods.

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