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Mind the gap! The mitochondrial control region and its power as a phylogenetic marker in echinoids

Overview of attention for article published in BMC Ecology and Evolution, May 2018
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Title
Mind the gap! The mitochondrial control region and its power as a phylogenetic marker in echinoids
Published in
BMC Ecology and Evolution, May 2018
DOI 10.1186/s12862-018-1198-x
Pubmed ID
Authors

Omri Bronstein, Andreas Kroh, Elisabeth Haring

Abstract

In Metazoa, mitochondrial markers are the most commonly used targets for inferring species-level molecular phylogenies due to their extremely low rate of recombination, maternal inheritance, ease of use and fast substitution rate in comparison to nuclear DNA. The mitochondrial control region (CR) is the main non-coding area of the mitochondrial genome and contains the mitochondrial origin of replication and transcription. While sequences of the cytochrome oxidase subunit 1 (COI) and 16S rRNA genes are the prime mitochondrial markers in phylogenetic studies, the highly variable CR is typically ignored and not targeted in such analyses. However, the higher substitution rate of the CR can be harnessed to infer the phylogeny of closely related species, and the use of a non-coding region alleviates biases resulting from both directional and purifying selection. Additionally, complete mitochondrial genome assemblies utilizing next generation sequencing (NGS) data often show exceptionally low coverage at specific regions, including the CR. This can only be resolved by targeted sequencing of this region. Here we provide novel sequence data for the echinoid mitochondrial control region in over 40 species across the echinoid phylogenetic tree. We demonstrate the advantages of directly targeting the CR and adjacent tRNAs to facilitate complementing low coverage NGS data from complete mitochondrial genome assemblies. Finally, we test the performance of this region as a phylogenetic marker both in the lab and in phylogenetic analyses, and demonstrate its superior performance over the other available mitochondrial markers in echinoids. Our target region of the mitochondrial CR (1) facilitates the first thorough investigation of this region across a wide range of echinoid taxa, (2) provides a tool for complementing missing data in NGS experiments, and (3) identifies the CR as a powerful, novel marker for phylogenetic inference in echinoids due to its high variability, lack of selection, and high compatibility across the entire class, outperforming conventional mitochondrial markers.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 143 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 143 100%

Demographic breakdown

Readers by professional status Count As %
Student > Bachelor 20 14%
Student > Ph. D. Student 18 13%
Researcher 18 13%
Student > Master 17 12%
Student > Doctoral Student 8 6%
Other 16 11%
Unknown 46 32%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 38 27%
Agricultural and Biological Sciences 33 23%
Environmental Science 8 6%
Unspecified 3 2%
Medicine and Dentistry 3 2%
Other 5 3%
Unknown 53 37%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 2. 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 September 2018.
All research outputs
#15,745,807
of 25,382,440 outputs
Outputs from BMC Ecology and Evolution
#2,638
of 3,714 outputs
Outputs of similar age
#192,431
of 344,275 outputs
Outputs of similar age from BMC Ecology and Evolution
#49
of 59 outputs
Altmetric has tracked 25,382,440 research outputs across all sources so far. This one is in the 37th percentile – i.e., 37% of other outputs scored the same or lower than it.
So far Altmetric has tracked 3,714 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 12.5. This one is in the 27th percentile – i.e., 27% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 344,275 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 42nd percentile – i.e., 42% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 59 others from the same source and published within six weeks on either side of this one. This one is in the 13th percentile – i.e., 13% of its contemporaries scored the same or lower than it.