A Post-pleistocene Calibrated Mutation Rate from Insect Museum Specimens
In this study two of the eighteen samples could not be sequenced successfully. These two samples were not the oldest, nor from the same locality. Severe degradation of DNA, beyond that in the other sixteen samples, or a mismatch in primer binding sites may account for failed amplification (Table 1). In those samples that were sequenced successfully ambiguities were high, while this is likely due to the degraded nature of aDNA, the coamplification of nuclear pseudogenes could also lead to such ambiguities. The amplification of relatively short (150 bp) segments increases the likelihood of amplifying pseudogenes, not amplifi...
Source: PLOS Currents Tree of Life - July 13, 2018 Category: Genetics & Stem Cells Authors: gdnwb3 Source Type: research
Chloroplast Genome Sequence Annotation of Dendrobium nobile (Asparagales: Orchidaceae), an Endangered Medicinal Orchid from Northeast India
Conclusion
Chloroplast genome sequences serve as valuable assets in herbal medicine. As many medicinal plants are highly endangered and rare in nature, little information is available to confirm their identity. Bio-barcodes derived from chloroplast genomes are quite useful for identifying species varieties and resources. Functional and structural annotations of gene content, gene organization, and chloroplast genome sequences have been used as important markers in systematic research. This report determined the complete chloroplast genome sequence of D. nobile from Northeast India. We found structural similarities among th...
Source: PLOS Currents Tree of Life - May 19, 2017 Category: Genetics & Stem Cells Authors: Devendra Biswal Source Type: research
Red Algal Phylogenomics Provides a Robust Framework for Inferring Evolution of Key Metabolic Pathways
Conclusion
Our phylogenomic analyses resulted in a well-supported red algal phylogeny that provides new insights into the evolution of red seaweeds. Our results will allow more accurate reconstruction of evolutionary events (e.g., gene family evolution2 and molecular calibration10) and provide a framework to map the distribution of red algal functions and traits. Further efforts are needed to substantiate the relationships among non-seaweed mesophilic red algae with high quality genome data from these taxa41.
Data Availability
The multi-protein alignment is available for download (ID: 20087) from TreeBASE (https://treebas...
Source: PLOS Currents Tree of Life - December 2, 2016 Category: Genetics & Stem Cells Authors: Huan Qiu Source Type: research
How Really Ancient Is Paulinella Chromatophora?
Introduction
Mitochondria and plastids evolved from freeliving bacteria by symbiogenesis more than one billion years ago1. Both events boosted the evolution of eukaryotes by expanding their metabolic abilities. Primary endosymbiosis leading to organelles (i.e., mitochondria and plastids) was thought to be unique in the history of life until the recent discovery of an independent primary endosymbiosis in Paulinella chromatophora2. This thecate filose amoeba hosts in its cytoplasm photosynthetic organelles of cyanobacterial origin, called chromatophores. Phylogenetic analysis of 16S rRNA showed that the chromatophores orig...
Source: PLOS Currents Tree of Life - March 15, 2016 Category: Genetics & Stem Cells Authors: ldelaye Source Type: research
Character State Reconstruction of Call Diversity in the Neoconocephalus Katydids Reveals High Levels of Convergence
We describe each species’ calls for the three call traits ‘call structure’, ‘pulse pattern’, and ‘pulse rate.’ The character states for these three call traits are listed in Table 1.
Table 1: Description of Neoconocephalus calls
The character states for the three call traits of the 17 species considered. C continuous, D discontinuous (=versed) call structure; Pulse rates < 100 Hz are classified as ‘slow’, > 100Hz as fast. The call structure in N. ensiger was equivocal, indicated by a ? (see text); * the verse duration for N. ensiger as given here...
Source: PLOS Currents Tree of Life - March 11, 2016 Category: Genetics & Stem Cells Authors: Katy Frederick Source Type: research
PhyloPen: Phylogenetic Tree Browsing Using a Pen and Touch Interface
Conclusions
Our objective is to develop an interactive phylogenetic tree-browsing user interface for experts that is more dynamic and ideally more natural than commonly used browsers, ultimately allowing the user to navigate, annotate, and change the tree structure with ease. In this work-in-progress, we tested an experimental pen- and touch-based interactive browser we developed called PhyloPen. Our preliminary formative evaluations show positive results, demonstrating some usefulness of pen and touch interfaces for phylogenetic trees. However, additional work based on our formative evaluations, including the revision of ...
Source: PLOS Currents Tree of Life - November 23, 2015 Category: Genetics & Stem Cells Authors: Anthony Wehrer Source Type: research
EAPhy: A Flexible Tool for High-throughput Quality Filtering of Exon-alignments and Data Processing for Phylogenetic Methods
Introduction
High-Throughput Sequencing (HTS) has revolutionised the field of phylogenetics by enabling researchers to question the evolutionary relationships between taxa with large-scale multi-locus datasets 1,2. The development of these methods has been driven by a realisation that the inclusion of many genetic markers helps to account for stochastic coalescent histories of individual genes 3,4,5,6. Species tree inference methods use the multispecies coalescent model to estimate potential gene tree – species tree discordance and large numbers of unlinked loci represent a greater sample of the gene tree distribution un...
Source: PLOS Currents Tree of Life - August 5, 2015 Category: Genetics & Stem Cells Authors: mblom Source Type: research
Visualising Geophylogenies in Web Maps Using GeoJSON
Discussion
At present the method described here requires a middle layer (written in PHP) that resides on a web server and converts the NEXUS file to GeoJSON. An obvious extension would be to port that code to Javascript and have the entire tool function within the web-browser client.
Although lacking some of the functionality of more specialised software such as GenGIS, an advantage of a web map-based tool is that it brings phylogenies into an environment already familiar to users of biodiversity data, such as the GBIF portal. Many users will have already encountered points on maps, and layers (e.g., of environmental d...
Source: PLOS Currents Tree of Life - June 23, 2015 Category: Genetics & Stem Cells Authors: Roderic Page Source Type: research
Concatenation Analyses in the Presence of Incomplete Lineage Sorting
This article has focused on what has been established theoretically for some standard methods for estimating species trees (i.e., concatenation using maximum likelihood and summary methods such as MP-EST and ASTRAL), as well as for the newer approach of weighted statistical binning, followed by a summary method. Because the term “statistical consistency” has been used in two different ways in the literature, we have summarized what is known under each meaning: the weaker sense where both parameters (sequence length per locus and number of loci) increase, and the stronger sense where only the number of loci incr...
Source: PLOS Currents Tree of Life - May 22, 2015 Category: Genetics & Stem Cells Authors: tandy Source Type: research
Concatenation and Species Tree Methods Exhibit Statistically Indistinguishable Accuracy under a Range of Simulated Conditions
Introduction
For decades, phylogeneticists have recognized the potential for discordance between a gene tree and its species tree 1,2. Maddison’s seminal insights on the topic 3 illustrate how discordance may arise from any of the following sources: gene duplication and extinction (“hidden paralogy”), lateral gene transfer, and incomplete lineage sorting (ILS). Given the computational and theoretical difficulties of adequately modeling gene descent, phylogeneticists have traditionally not attempted to reconstruct species phylogenies with models that explicitly account for sources of gene trees-species tree discord, a...
Source: PLOS Currents Tree of Life - March 9, 2015 Category: Genetics & Stem Cells Authors: jtonini Source Type: research
Correction: Building a Phylogenomic Pipeline for the Eukaryotic Tree of Life – Addressing Deep Phylogenies with Genome-Scale Data
Correction
In table 1 an incorrect value was provided for the “Contigs” value for “Filamoeba nolandi” (Column 3, row 2). The corrected table is provided below:
Table 1: Transcriptome statistics for Amoebozoa used in case study.
Taxon
ATCC
Contigs
SSU
Bacterial
Eukaryotic
Unknown
Genes
Filamoeba nolandi
50430
21671
17
2409
12205
7057
171
Pessonella sp.
PRA29
17104
31
1783
8695
6626
199
Trichosphaerium sp.
40318
22137
15
2252
9541
10344
35
Eukaryota sp. JRG-2011
50979
14754
33
1940
7303
5478
178
Stereomyxa ramosa
50982
21354
38
2141
9854
9321
210
Reference
Grant JR, Katz LA. Buildin...
Source: PLOS Currents Tree of Life - March 6, 2015 Category: Genetics & Stem Cells Authors: ploscurrents Source Type: research
Correction: Building a Phylogenomic Pipeline for the Eukaryotic Tree of Life – Addressing Deep Phylogenies with Genome-Scale Data
Correction
In table 1 an incorrect value was provided for the “Contigs” value for “Filamoeba nolandi” (Column 3, row 2). The corrected table is provided below:
Table 1: Transcriptome statistics for Amoebozoa used in case study.
Taxon
ATCC
Contigs
SSU
Bacterial
Eukaryotic
Unknown
Genes
Filamoeba nolandi
50430
21671
17
2409
12205
7057
171
Pessonella sp.
PRA29
17104
31
1783
8695
6626
199
Trichosphaerium sp.
40318
22137
15
2252
9541
10344
35
Eukaryota sp. JRG-2011
50979
14754
33
1940
7303
5478
178
Stereomyxa ramosa
50982
21354
38
2141
9854
9321
210
Reference
Grant JR, Katz LA...
Source: PLOS Currents Tree of Life - March 6, 2015 Category: Genetics & Stem Cells Authors: ploscurrents Source Type: research
One Tree to Link Them All: A Phylogenetic Dataset for the European Tetrapoda
Conclusion
We provide here a phylogenetic dataset constituted of 100 chronograms of European Tetrapoda species as a tool for ecological studies that aim to incorporate an evolutionary perspective, and for phylogenetic conservation assessment. This phylogenetic dataset is in general agreement with previous studies, and we expect it to be coarsely approximate with the “true” Tetrapoda evolutionary tree. Instead of providing the best ML tree for every group, we provide 100 trees (available on Dryad repository), as computing analyses with several trees allows taking in account phylogenetic uncertainty. Regarding th...
Source: PLOS Currents Tree of Life - August 8, 2014 Category: Genetics & Stem Cells Authors: Cristina Roquet Source Type: research
DNA Barcoding of Marine Copepods: Assessment of Analytical Approaches to Species Identification
Conclusions
This study presents new DNA barcode data for marine copepods (800 sequences for 63 species not previously sequenced) and reports the results of new analyses of a larger dataset (1,381 sequences for 195 copepod species). Our conclusions include recommendations to improve the accuracy and feasibility of using DNA barcodes for species identification of marine planktonic copepods, including: 1) availability of PCR and sequencing primers suited to the targeted species; 2) availability of a taxonomically-comprehensive DNA barcode database linking DNA sequences to accurately identified specimens; 3) increased density ...
Source: PLOS Currents Tree of Life - June 23, 2014 Category: Genetics & Stem Cells Authors: leocadio Source Type: research
Best Practices for Data Sharing in Phylogenetic Research
Introduction
The amount of phylogenetic data has rapidly increased in its quality and availability over the past few decades. Additionally, phylogenetic matrices and trees are often based on and need to be linked to data on traits, geographic distribution, and genetic / genomic sequences. Despite the rapid growth in data generation, comparative data from published studies are too often unavailable, incomplete, or incompatible thereby greatly limiting reproducibility and expansion of existing studies 1,2. A greater focus on data integration and interoperability, even at the data collection phase of a project, allows for sca...
Source: PLOS Currents Tree of Life - June 19, 2014 Category: Genetics & Stem Cells Authors: Karen Cranston Source Type: research
