TY - JOUR
T1 - Phylogeny of terraranan frogs based on 2,665 loci and impacts of missing data on phylogenomic analyses
AU - Barrientos, Lucas S.
AU - Streicher, Jeffrey W.
AU - Miller, Elizabeth C.
AU - Pie, Marcio R.
AU - Wiens, John J.
AU - Crawford, Andrew J.
N1 - Funding Information:
This work was supported by Colciencias under grant number 567 for PhD studies; Universidad de los Andes through a Crédito Condonable; Universidad de los Andes FAPA fund; and U.S. National Science Foundation grant DEB 1655690. We are grateful for tissue loans from the museum collections cited in the methods. Thanks to IT Management and ExaCore of the Office of the Vice President for Research & Creation at the Universidad de Los Andes for high-performance computing services and technical assistance. We thank Andres M. Cuervo, Luisa Dueñas, Carlos E. Guarnizo, Santiago Herrera, Andrea Paz, Camila Plata, Evan Twomey and two anonymous reviewers for providing valuable comments on earlier versions of this manuscript. Special thanks to David O. Botero, Catalina Ramírez-Portilla, and Fanny Gonzáles for help with script writing and bioinformatic advice. Thanks to Carolina Amorocho and Luisa Castellanos for help in the lab and with paperwork. We thank Jorge Avendaño for his advice with the figures.
Publisher Copyright:
© The Trustees of the Natural History Museum, London 2021. All Rights Reserved.
PY - 2021
Y1 - 2021
N2 - Terraranae is a large clade of New World direct-developing frogs that includes 3–5 families and >1,100 described species (∼15% of all named frog species). The relationships among major groups of terraranan frogs have been highly contentious, including conflicts among four recent phylogenomic studies utilizing 95, 220, 389, and 2,214 nuclear loci, respectively. In this paper, we re-evaluate relationships within Terraranae using a novel genomic dataset for 16 ingroup species representing most terraranan families and subfamilies. The preferred data matrix consisted of 2,665 nuclear loci from ultraconserved elements (UCEs), with a total of 743,419 aligned base pairs and 57% missing data. Concatenated likelihood analyses and coalescent-based species-tree analyses recovered strong statistical support for the following relationships among terraranan families: (Brachycephalidae, (Eleutherodactylidae, (Craugastoridae + ‘Strabomantidae’))). This position for Brachycephalidae agrees with two previous phylogenomic studies but conflicts with two others. Our results infer Strabomantis (of the Strabomantidae) to be with (or within) Craugastor (Craugastoridae), rather than with other strabomantid genera. This renders Strabomantidae paraphyletic with respect to Craugastoridae. Our results also suggest that Pristimantinae is paraphyletic with respect to Holoadeninae. We also find that using matrices with less missing data (and concomitantly fewer UCE loci) generally resulted in trees with lower mean branch support and problematic phylogenies (e.g. non-monophyly of terraranans). Overall, our results help resolve controversial relationships within one of the largest clades of frogs, with a dataset including ∼7 times more loci than those used in previous studies focused on this clade.
AB - Terraranae is a large clade of New World direct-developing frogs that includes 3–5 families and >1,100 described species (∼15% of all named frog species). The relationships among major groups of terraranan frogs have been highly contentious, including conflicts among four recent phylogenomic studies utilizing 95, 220, 389, and 2,214 nuclear loci, respectively. In this paper, we re-evaluate relationships within Terraranae using a novel genomic dataset for 16 ingroup species representing most terraranan families and subfamilies. The preferred data matrix consisted of 2,665 nuclear loci from ultraconserved elements (UCEs), with a total of 743,419 aligned base pairs and 57% missing data. Concatenated likelihood analyses and coalescent-based species-tree analyses recovered strong statistical support for the following relationships among terraranan families: (Brachycephalidae, (Eleutherodactylidae, (Craugastoridae + ‘Strabomantidae’))). This position for Brachycephalidae agrees with two previous phylogenomic studies but conflicts with two others. Our results infer Strabomantis (of the Strabomantidae) to be with (or within) Craugastor (Craugastoridae), rather than with other strabomantid genera. This renders Strabomantidae paraphyletic with respect to Craugastoridae. Our results also suggest that Pristimantinae is paraphyletic with respect to Holoadeninae. We also find that using matrices with less missing data (and concomitantly fewer UCE loci) generally resulted in trees with lower mean branch support and problematic phylogenies (e.g. non-monophyly of terraranans). Overall, our results help resolve controversial relationships within one of the largest clades of frogs, with a dataset including ∼7 times more loci than those used in previous studies focused on this clade.
KW - Anura
KW - Terraranae
KW - amphibians
KW - missing data
KW - phylogenomics
KW - ultraconserved elements
UR - http://www.scopus.com/inward/record.url?scp=85108271431&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85108271431&partnerID=8YFLogxK
U2 - 10.1080/14772000.2021.1933249
DO - 10.1080/14772000.2021.1933249
M3 - Article
AN - SCOPUS:85108271431
VL - 19
SP - 818
EP - 833
JO - Systematics and Biodiversity
JF - Systematics and Biodiversity
SN - 1477-2000
IS - 7
ER -