Ultraconserved elements resolve the phylogeny and corroborate patterns of molecular rate variation in herons (Aves: Ardeidae)
Abstract
Thoroughly sampled and well-supported phylogenetic trees are essential to taxonomy and to guide studies of evolution and ecology. Despite extensive prior inquiry, a comprehensive tree of heron relationships (Aves: Ardeidae) has not yet been published. As a result, the classification of this family remains unstable, and their evolutionary history remains poorly studied. Here, we sample genome-wide ultraconserved elements (UCEs) and mitochondrial DNA sequences (mtDNA) of >90% of extant species to estimate heron phylogeny using a combination of maximum likelihood, coalescent, and Bayesian inference methods. The UCE and mtDNA trees are mostly concordant with one another, providing a topology that resolves relationships among the 5 heron subfamilies and indicates that the genera Gorsachius, Botaurus, Ardea, and Ixobrychus are not monophyletic. We also present the first genetic data from the Forest Bittern Zonerodius heliosylus, an enigmatic species of New Guinea; our results suggest that it is a member of the genus Ardeola and not the Tigrisomatinae (tiger herons), as previously thought. Finally, we compare molecular rates between heron clades in the UCE tree with those in previously constructed mtDNA and DNA–DNA hybridization trees. We show that rate variation in the UCE tree corroborates rate patterns in the previously constructed trees—that bitterns (Ixobrychus and Botaurus) evolved comparatively faster, and some tiger herons (Tigrisoma) and the Boat-billed Heron (Cochlearius)…
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In other bird groups, higher level relationships have been largely resolved by sequencing large numbers of genes, either via genome reduction methods (e.g., Ultraconserved Elements, UCEs) or mining data from whole genome sequencing.
“In other bird groups, higher level relationships have been largely resolved by sequencing large numbers of genes, either via genome reduction methods (e.g., Ultraconserved Elements, UCEs) or mining data from whole genome sequencing (Prum et al., 2015;Chen et al., 2021;Hruska et al., 2023).”
From Enigmas no longer: using ultraconserved elements to place several unusual hawk taxa and address the non-monophyly of the genus <i>Accipiter</i> (Accipitriformes: Accipitridae) (2025) · cites this paper as Hruska et al., 2023
Cites
Posterior summarization in Bayesian phylogenetics using tracer 1.7
Rambaut, A., Drummond, A. J., Xie, D., Baele, G., & Suchard, M. A. (2018) · Systematic Biology · doi:10.1093/sysbio/syy032 · Cited by 11,159 · see citing works
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
Bouckaert, R., Vaughan, T. G., Barido-Sottani, J., Duchêne, S., Fourment, M., Gavryushkina, A., Heled, J., Jones, G., Kühnert, D., De Maio, N., et al. (2019) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1006650 · Cited by 4,556 · see citing works
Body size, metabolic rate, generation time, and the molecular clock.
Martin, A. P., & Palumbi, S. R. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.9.4087 · Cited by 1,239 · cited 1× · see citing works
“…suggestions, including differences between taxa in metabolic rate, generation time, rate of germ cell division, body temperature, DNA repair efficiency, population size, and clade size (Martin and Palumbi 1993, Sheldon and Bledsoe 1993, Rand 1994, Omland 1997, Bleiweiss 1998, and Gillooly et al.”
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Catanach, T. A., Halley, M. R., & Pirro, S. (2025) · Biological Journal of the Linnean Society · doi:10.1093/biolinnean/blae028 · Cited by 76 · see citing works
- Authors
- Hruska, J. P., Holmes, J., Oliveros, C., Shakya, S., Lavretsky, P., McCracken, K. G., Sheldon, F. H., & Moyle, R. G.
- Affiliations
- Texas Tech University (US)
- University of Kansas (US)
- Louisiana State University (US)
- The University of Texas at El Paso (US)
- University of Miami (US)
- Corresponding author
- Hruska, Jack P
- ORCID
- Venue
- Ornithology
- Publisher
- Oxford University Press (OUP)
- Published
- 2023-01-22
- Volume
- 140
- Issue
- 2
- ISSN
- 2732-4613 (ISSN-L)
- 0004-8038
- OpenAlex
- W4317704433
- Cited by
- 37
- References
- 3
- Citations by year
- 2026: 4 · 2025: 5 · 2024: 21 · 2023: 7
- FWCI
- 3.56
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- The Auk (publishedVersion)
- Funders
- National Science Foundation (DEB-1557053)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- herons, ultraconserved elements, phylogeny, mitochondrial DNA, monophyly, Ardea
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