High utility of Ultraconserved Elements (UCE) for disentangling
the elusive relationships of tarantulas

J 2023

High utility of Ultraconserved Elements (UCE) for disentangling the elusive relationships of tarantulas

ORTIZ MARTÍNEZ, David

Základní údaje

Originální název

High utility of Ultraconserved Elements (UCE) for disentangling the elusive relationships of tarantulas

Autoři

ORTIZ MARTÍNEZ, David (724 Španělsko, garant, domácí)

Vydání

Zoologica Scripta, Wiley, 2023, 0300-3256

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10613 Zoology

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 2.300

Kód RIV

RIV/00216224:14310/23:00132088

Organizační jednotka

Přírodovědecká fakulta

DOI

http://dx.doi.org/10.1111/zsc.12619

UT WoS

001022144900001

EID Scopus

2-s2.0-85164603158

Klíčová slova anglicky

concordance factor; Mygalomorphae; phylogenomics; Theraphosidae; UCE data mining

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 22. 12. 2023 08:32, Mgr. Marie Novosadová Šípková, DiS.

Anotace

V originále

Although tarantulas are a widespread, highly diversified, and charismatic spider group, our understanding of their evolution remains limited. A recent transcriptome-based approach, including 16% of the nominal tarantula genera (25), provided the first robust phylogenetic hypothesis of deep tarantula relationships. However, transcriptomics has practical downsides, making it less than ideal for phylogenomic analyses. Ultraconserved Elements (UCE) sequencing, a cost-effective alternative, allows for the simultaneous reading of hundreds of loci and utilizing samples with degraded DNA, including museum material, but its utility for resolving deep tarantula relationships remains to be tested. In this study, I recovered up to similar to 850 unique UCE loci from publicly available individual tarantula transcriptomes. Phylogenetic estimation using these loci resulted in topologies identical to those obtained from the published complete transcriptomic datasets, with limited phylogenetic uncertainty restricted to two branches in the tarantula tree of life. I conclude that UCE information has great potential for resolving at least moderate to deep tarantula relationships and that numerous UCE loci can be harvested from tarantula transcriptomic data. Finally, I provide databases of transcripts and UCE loci for the 27 currently available tarantula genera, facilitating their inclusion in future phylogenomic studies with deeper taxon coverage.

Návaznosti

LM2018140, projekt VaV

Název: e-Infrastruktura CZ (Akronym: e-INFRA CZ)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, e-Infrastruktura CZ

Citovat

ORTIZ MARTÍNEZ, David. High utility of Ultraconserved Elements (UCE) for disentangling the elusive relationships of tarantulas. Zoologica Scripta. Wiley, 2023, roč. 52, č. 6, s. 645-653. ISSN 0300-3256. Dostupné z: https://dx.doi.org/10.1111/zsc.12619.

@article{2332978,
   author = {Ortiz Martínez, David},
   article_number = {6},
   doi = {http://dx.doi.org/10.1111/zsc.12619},
   keywords = {concordance factor; Mygalomorphae; phylogenomics; Theraphosidae; UCE data mining},
   language = {eng},
   issn = {0300-3256},
   journal = {Zoologica Scripta},
   title = {High utility of Ultraconserved Elements (UCE) for disentangling the elusive relationships of tarantulas},
   url = {https://doi.org/10.1111/zsc.12619},
   volume = {52},
   year = {2023}
}

TY  - JOUR
ID  - 2332978
AU  - Ortiz Martínez, David
PY  - 2023
TI  - High utility of Ultraconserved Elements (UCE) for disentangling the elusive relationships of tarantulas
JF  - Zoologica Scripta
VL  - 52
IS  - 6
SP  - 645-653
EP  - 645-653
PB  - Wiley
SN  - 03003256
KW  - concordance factor
KW  - Mygalomorphae
KW  - phylogenomics
KW  - Theraphosidae
KW  - UCE data mining
UR  - https://doi.org/10.1111/zsc.12619
N2  - Although tarantulas are a widespread, highly diversified, and charismatic spider group, our understanding of their evolution remains limited. A recent transcriptome-based approach, including 16% of the nominal tarantula genera (25), provided the first robust phylogenetic hypothesis of deep tarantula relationships. However, transcriptomics has practical downsides, making it less than ideal for phylogenomic analyses. Ultraconserved Elements (UCE) sequencing, a cost-effective alternative, allows for the simultaneous reading of hundreds of loci and utilizing samples with degraded DNA, including museum material, but its utility for resolving deep tarantula relationships remains to be tested. In this study, I recovered up to similar to 850 unique UCE loci from publicly available individual tarantula transcriptomes. Phylogenetic estimation using these loci resulted in topologies identical to those obtained from the published complete transcriptomic datasets, with limited phylogenetic uncertainty restricted to two branches in the tarantula tree of life. I conclude that UCE information has great potential for resolving at least moderate to deep tarantula relationships and that numerous UCE loci can be harvested from tarantula transcriptomic data. Finally, I provide databases of transcripts and UCE loci for the 27 currently available tarantula genera, facilitating their inclusion in future phylogenomic studies with deeper taxon coverage.
ER  -

ORTIZ MARTÍNEZ, David. High utility of Ultraconserved Elements (UCE) for disentangling the elusive relationships of tarantulas. \textit{Zoologica Scripta}. Wiley, 2023, roč.~52, č.~6, s.~645-653. ISSN~0300-3256. Dostupné z: https://dx.doi.org/10.1111/zsc.12619.

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