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Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

Overview of attention for article published in BMC Evolutionary Biology, August 2015
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  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (87th percentile)

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23 tweeters

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Title
Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants
Published in
BMC Evolutionary Biology, August 2015
DOI 10.1186/s12862-015-0423-0
Pubmed ID
Authors

Stephen A Smith, Michael J Moore, Joseph W Brown, Ya Yang

Abstract

The use of transcriptomic and genomic datasets for phylogenetic reconstruction has become increasingly common as researchers attempt to resolve recalcitrant nodes with increasing amounts of data. The large size and complexity of these datasets introduce significant phylogenetic noise and conflict into subsequent analyses. The sources of conflict may include hybridization, incomplete lineage sorting, or horizontal gene transfer, and may vary across the phylogeny. For phylogenetic analysis, this noise and conflict has been accommodated in one of several ways: by binning gene regions into subsets to isolate consistent phylogenetic signal; by using gene-tree methods for reconstruction, where conflict is presumed to be explained by incomplete lineage sorting (ILS); or through concatenation, where noise is presumed to be the dominant source of conflict. The results provided herein emphasize that analysis of individual homologous gene regions can greatly improve our understanding of the underlying conflict within these datasets. Here we examined two published transcriptomic datasets, the angiosperm group Caryophyllales and the aculeate Hymenoptera, for the presence of conflict, concordance, and gene duplications in individual homologs across the phylogeny. We found significant conflict throughout the phylogeny in both datasets and in particular along the backbone. While some nodes in each phylogeny showed patterns of conflict similar to what might be expected with ILS alone, the backbone nodes also exhibited low levels of phylogenetic signal. In addition, certain nodes, especially in the Caryophyllales, had highly elevated levels of strongly supported conflict that cannot be explained by ILS alone. This study demonstrates that phylogenetic signal is highly variable in phylogenomic data sampled across related species and poses challenges when conducting species tree analyses on large genomic and transcriptomic datasets. Further insight into the conflict and processes underlying these complex datasets is necessary to improve and develop adequate models for sequence analysis and downstream applications. To aid this effort, we developed the open source software phyparts ( https://bitbucket.org/blackrim/phyparts ), which calculates unique, conflicting, and concordant bipartitions, maps gene duplications, and outputs summary statistics such as internode certainy (ICA) scores and node-specific counts of gene duplications.

Twitter Demographics

The data shown below were collected from the profiles of 23 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 223 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 4 2%
Portugal 1 <1%
Germany 1 <1%
Mexico 1 <1%
Brazil 1 <1%
Spain 1 <1%
Estonia 1 <1%
Unknown 213 96%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 50 22%
Researcher 41 18%
Student > Master 23 10%
Student > Doctoral Student 20 9%
Student > Bachelor 14 6%
Other 35 16%
Unknown 40 18%
Readers by discipline Count As %
Agricultural and Biological Sciences 122 55%
Biochemistry, Genetics and Molecular Biology 41 18%
Computer Science 5 2%
Environmental Science 2 <1%
Earth and Planetary Sciences 2 <1%
Other 5 2%
Unknown 46 21%

Attention Score in Context

This research output has an Altmetric Attention Score of 12. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 26 August 2018.
All research outputs
#1,566,855
of 15,607,540 outputs
Outputs from BMC Evolutionary Biology
#500
of 2,702 outputs
Outputs of similar age
#29,129
of 236,838 outputs
Outputs of similar age from BMC Evolutionary Biology
#1
of 1 outputs
Altmetric has tracked 15,607,540 research outputs across all sources so far. Compared to these this one has done well and is in the 89th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 2,702 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 10.5. This one has done well, scoring higher than 81% of its peers.
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