Utilizing paralogues for phylogenetic reconstruction has the potential to increase species tree support and reduce gene tree discordance in target enrichment data
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F67985939%3A_____%2F22%3A00562206" target="_blank" >RIV/67985939:_____/22:00562206 - isvavai.cz</a>
Alternative codes found
RIV/00216208:11310/22:10457437
Result on the web
<a href="https://doi.org/10.1111/1755-0998.13684" target="_blank" >https://doi.org/10.1111/1755-0998.13684</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1111/1755-0998.13684" target="_blank" >10.1111/1755-0998.13684</a>
Alternative languages
Result language
angličtina
Original language name
Utilizing paralogues for phylogenetic reconstruction has the potential to increase species tree support and reduce gene tree discordance in target enrichment data
Original language description
The analysis of target enrichment data in phylogenetics lacks optimization toward using paralogues for phylogenetic reconstruction. We developed a novel approach of detecting paralogues and utilizing them for phylogenetic tree inference, by retrieving both ortho- and paralogous copies and creating orthologous alignments, from which the gene trees are built. We implemented this approach in ParalogWizard and demonstrate its performance in plant groups that underwent a whole genome duplication relatively recently: the subtribe Malinae (family Rosaceae), using Angiosperms353 as well as Malinae481 probes, the genus Oritrophium (family Asteraceae), using Compositae1061 probes, and the genus Amomum (family Zingiberaceae), using Zingiberaceae1180 probes. Discriminating between orthologues and paralogues reduced gene tree discordance and increased the species tree support in the case of the Malinae, but not for Oritrophium and Amomum. This may relate to the difference in the proportion of paralogous loci between the data sets, which was highest for the Malinae. Overall, retrieving paralogues for phylogenetic reconstruction following ParalogWizard has the potential to increase the species tree support and reduce gene tree discordance in target enrichment data, particularly if the proportion of paralogous loci is high.
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
Result was created during the realization of more than one project. More information in the Projects tab.
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 Ecology Resources
ISSN
1755-098X
e-ISSN
1755-0998
Volume of the periodical
22
Issue of the periodical within the volume
8
Country of publishing house
GB - UNITED KINGDOM
Number of pages
17
Pages from-to
3018-3034
UT code for WoS article
000832570100001
EID of the result in the Scopus database
2-s2.0-85135114319