Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60077344%3A_____%2F22%3A00553923" target="_blank" >RIV/60077344:_____/22:00553923 - isvavai.cz</a>
Result on the web
<a href="https://www.sciencedirect.com/science/article/pii/S1055790322000458/pdfft?md5=f64da963ec4b88ba7cb52a81433d45d8&pid=1-s2.0-S1055790322000458-main.pdf" target="_blank" >https://www.sciencedirect.com/science/article/pii/S1055790322000458/pdfft?md5=f64da963ec4b88ba7cb52a81433d45d8&pid=1-s2.0-S1055790322000458-main.pdf</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1016/j.ympev.2022.107432" target="_blank" >10.1016/j.ympev.2022.107432</a>
Alternative languages
Result language
angličtina
Original language name
Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses
Original language description
Target sequence capture has emerged as a powerful method to sequence hundreds or thousands of genomic regions in a cost- and time-efficient approach. In most cases, however, targeted regions lack full sequence information for certain samples, due to taxonomic, laboratory, or stochastic factors. Loci lacking molecular data for a large number of samples are commonly excluded from downstream analyses, even though they may still contain valuable information. On the other hand, including data-poor loci may bias phylogenetic analyses. Here we use a target sequence capture dataset of an ecologically and taxonomically diverse group of spiny sunflowers (Asteraceae, or Compositae: Barnadesioideae) to test how the inclusion or exclusion of such data-poor loci affects phylogenetic inference. We investigate the sensitivity of concatenation and coalescent approaches to missing data with matrices of varying taxonomic completeness by filtering loci with different proportions of missing samples prior to data analysis. We find that missing data affect both the topology and branch support of the resulting phylogenies. The matrix containing all loci yielded the overall highest node support values, independently of the amount of missing nucleotides. These results provide empirical support to earlier suggestions based on single genes and data simulations that taxa with high amounts of missing data should not be readily dismissed as they can provide essential information for phylogenomic reconstruction.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10611 - Plant sciences, botany
Result continuities
Project
<a href="/en/project/EF18_053%2F0016982" target="_blank" >EF18_053/0016982: International mobilities for researchers and administrative employees of Biology Centre</a><br>
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2022
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Molecular Phylogenetics and Evolution
ISSN
1055-7903
e-ISSN
1095-9513
Volume of the periodical
169
Issue of the periodical within the volume
APR 01
Country of publishing house
US - UNITED STATES
Number of pages
12
Pages from-to
107432
UT code for WoS article
000820603200007
EID of the result in the Scopus database
2-s2.0-85124584372