A phylogenomic supermatrix of Galliformes (Landfowl) reveals biased branch lengths
Abstract
Building taxon-rich phylogenies is foundational for macroevolutionary studies. One approach to improve taxon sampling beyond individual studies is to build supermatricies of publicly available data, incorporating taxa sampled across different studies and utilizing different loci. Most existing supermatrix studies have focused on loci commonly sequenced with Sanger technology ("legacy" markers, such as mitochondrial data and small numbers of nuclear loci). However, incorporating phylogenomic studies into supermatrices allows problem nodes to be targeted and resolved with considerable amounts of data, while improving taxon sampling with legacy data. Here we estimate phylogeny from a galliform supermatrix which includes well-known model and agricultural species such as the chicken and turkey. We assembled a supermatrix comprising 4500 ultra-conserved elements (UCEs) collected as part of recent phylogenomic studies in this group and legacy mitochondrial and nuclear (intron and exon) sequences. Our resulting phylogeny included 88% of extant species and recovered well-accepted relationships with strong support. However, branch lengths, which are particularly important in down-stream macroevolutionary studies, appeared vastly skewed. Taxa represented only by rapidly evolving mitochondrial data had high proportions of missing data and exhibited long terminal branches. Conversely, taxa sampled for slowly evolving UCEs with low proportions of missing data exhibited substantially shorter terminal branches. We explored several branch length re-estimation methods with particular attention to terminal branches and conclude that re-estimation using well-sampled mitochondrial sequences may be a pragmatic approach to obtain trees suitable for macroevolutionary analysis.
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New methods have been developed to combine 'legacy markers' (i.e., Sanger data) with datasets obtained via next generation sequencing (NGS) analyses.
“Furthermore, to deal with the scarcity of tissue samples, new methods have been developed to combine”
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 Kimball et al., 2021
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“[33] which consisted of 264 species of Galliformes (88% of the order, and at least 85% of each family): 160 species within Phasianidae and 104 species outside Phasianidae, based on the IOC taxonomy v10.”
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“Neither of the two species of Goniodes treated here appears to be closely related to other goniodid lice on related hosts (eg the genera Afropavo, Argusianus, and Rheinardia Maingonnat, 1882; Wang et al. 2014; Chen et al. 2021; Kimball et al. 2021).”
BackgroundMethodInfluentialGustafsson, D. R., Tian, C., Ren, M., et al. (2024) · Deutsche Entomologische Zeitschrift · doi:10.3897/dez.71.111874 · Cited by 5 · see citing works
“For instance, there appears to be little overlap between the lice of megapodiid hosts and other landfowl (Table 2), likely reflecting that megapodiids are the sis - ter group of all other galliforms (Kimball et al. 2021).”
BackgroundInfluentialZelenkov, N. V., Паластрова, Е. С., Martynovich, N., et al. (2023) · Biological Communications · doi:10.21638/spbu03.2023.406 · Cited by 5 · see citing works
Zelenkov, N. V. (2024) · Paleontological Journal · doi:10.1134/s0031030124010106 · Cited by 5 · see citing works
“At the same time, molecular phylogenetic studies clearly reconstruct grouse as a fairly advanced Phasianidae subclade sister to turkeys (Lucchini et al., 2001; Dimcheff et al., 2002; Drovetski, 2002; Kimball et al., 2021a, 2021b).”
Mitogenomic Insights into the Evolution, Divergence Time, and Ancestral Ranges of Coturnix Quails
Dey, P., Ray, S. D., Kochiganti, V. H. S., Pukazhenthi, B. S., Koepfli, K., & Singh, R. P. (2024) · Genes · doi:10.3390/genes15060742 · Cited by 5 · see citing works
“The estimated divergence of C. chinensis and C. ypsilophora at approximately 8.59 Ma suggests that the possible timeframe for their long-distance dispersal events from the Oriental zone to the Australian landmass likely occurred during the late Miocene period.”
BackgroundInfluentialZhou, C., Zheng, X., Feng, K., Peng, K., Zhang, Y., Zhao, G., Meng, Y., Zhang, L., Yue, B., & Wu, Y. (2022) · Journal of Heredity · doi:10.1093/jhered/esac069 · Cited by 5 · see citing works
A Comparison of Telencephalon Composition among Chickens, Junglefowl, and Wild Galliforms
Racicot, K. J., Ham, J. R., Augustine, J. K., Henriksen, R., Wright, D., & Iwaniuk, A. N. (2024) · Brain Behavior and Evolution · doi:10.1159/000537844 · Cited by 4 · see citing works
“Second, we used grouse as our “ wild-type ” [39], but obtaining these species in the wild is extremely dif fi cult.”
BackgroundMethodWang, P., Liu, S., Hu, J., et al. (2022) · Journal of Avian Biology · doi:10.1111/jav.02979 · Cited by 4 · see citing works
Sharma, S., & Kumar, S. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac236 · Cited by 4 · see citing works
“…nucleus) (Kimball et al. 2021), specific codon positions (Dos Reis et al. 2018), functional annotations (e.g., coding and noncoding) (Thode et al. 2020; Kimball et al. 2021), and prior biological and evolutionary features (Prasanna et al. 2020; Vasilikopoulos et al. 2020; Haelewaters et al. 2021).”
BackgroundGustafsson, D. R., & Zou, F. (2023) · Zootaxa · doi:10.11646/zootaxa.5284.3.3 · Cited by 4 · see citing works
Nadal, J., Sáez, D., Volponi, S., et al. (2024) · Environmental Monitoring and Assessment · doi:10.1007/s10661-023-12277-4 · Cited by 4 · see citing works
“This species boasts an ancient phylogenetic origin (Kimball et al. 2021; Wang et al. 2017), sharing migratory patterns, behavioral traits, and genetic characteristics with numerous contemporary Afro-Palearctic bird species (Haest et al. 2020).”
Exploring potentialities of avian genomic research in Nepalese Himalayas
Ghimire, P., Dahal, N., Karna, A. K., Karki, S., & Lamichhaney, S. (2021) · Avian Research · doi:10.1186/s40657-021-00290-5 · Cited by 4 · see citing works
Zhao, M., Kimball, R. T., & Braun, E. L. (2026) · Zoologica Scripta · doi:10.1111/zsc.70047 · Cited by 4 · see citing works
“In some cases, taxa with poor sequence recovery appear to have exceptionally long terminal branches (e.g., Bernstein and Ruane 2022; Braun et al. 2024; Derkarabetian et al. 2019; Kimball et al. 2021; McCullough et al. 2025; Nash et al. 2024; Zhao, Oswald, et al. 2025).”
Self-citationEleiwa, A., Nadal, J., Vilaprinyó, E., Marı́n-Sanguino, A., Albert Sorribas, B., Basallo, O., Lucido, A., Richart, C., Pena, R. N., Ros‐Freixedes, R., et al. (2024) · Scientific Reports · doi:10.1038/s41598-024-70018-0 · Cited by 3 · see citing works
Crowe, T. M., Mandiwana-Neudani, T. G., Little, R. M., et al. (2022) · Ostrich · doi:10.2989/00306525.2022.2120921 · Cited by 3 · see citing works
“All these findings have been confirmed by subsequent molecular phylogenetic research using extensive genomic datasets (Wang et al. 2013; Kimball et al. 2021).”
BackgroundTaphonomic damage obfuscates interpretation of the retroarticular region of the Asteriornis mandiblePreprint
Crane, A., Benito, J., Chen, A. S., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.06.13.544555 · Cited by 3 · see citing works
“…optimality criteria with molecular scaffolds derived from previous studies (Hackett et al., 2008; Gonzalez et al., 2009; Harris et al., 2014; Jarvis et al., 2014; Prum et al., 2015; Reddy et al., 2017; Kimball et al., 2019; Kimball et al., 2021; Kuhl et al., 2021; Simmons et al., 2022).”
Abrha, A. M., Rödder, D., Gedeon, K., et al. (2025) · Ornithology Research · doi:10.1007/s43388-025-00252-1 · Cited by 2 · see citing works
“Most galliform species (megapodes, guans, guineafowls, New World quails, and pheasants and allies) (Winkler et al. 2015; Kimball et al. 2021 ) are weak fliers, but rather excellent runners (Heers 2018).”
Different Evolutionary Trends of Galloanseres: Mitogenomics Analysis
Zhou, S., Wang, X., Wang, L., Gao, X., Lyu, T., Xia, T., Shi, L., Dong, Y., Mei, X., Zhang, Z., et al. (2024) · Animals · doi:10.3390/ani14101437 · Cited by 2 · see citing works
Gustafsson, D. R., Tian, C., Ren, M., et al. (2024) · European Journal of Taxonomy · doi:10.5852/ejt.2024.968.2703 · Cited by 2 · see citing works
“Species of Goniocotes are known from at least some of the hosts in each of the three divisions of Phasianidae Horsfield, 1821 by Kimball et al. (2021), as well as on Numididae de Sélys Longchamps, 1842 and Megapodiidae Lesson, 1831.”
BackgroundPhylogenomics and comparative genomic perspective on the avian radiation
Chen, G., Xie, Y., & Zhang, G. (2025) · Nature Reviews Biodiversity · doi:10.1038/s44358-025-00062-9 · Cited by 3 · see citing works
“used in studies of bird phylogeny to resolve relationships at multiple taxonomic levels, from phylogeny within specific genera 55–57 , across families 58–61 , and within deeper evolution trees across avian orders 62,63 .”
Macroevolutionary drivers of morphological disparity in the avian quadratePreprint
Kuo, P.-C., Navalón, G., Benson, R., & Field, D. J. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.05.561045 · Cited by 2 · see citing works
Fonseca-Cortés, A., Zhang, R., Cardoso, D., et al. (2026) · Botanical Journal of the Linnean Society · doi:10.1093/botlinnean/boag018 · Cited by 1 · see citing works
Mei, Q., Deng, Y., Zhao, D., et al. (2024) · Genes · doi:10.3390/genes15121569 · Cited by 1 · see citing works
“In the case of Phasianus , specific PCGs like CO I , CO II , CO III , ND1 , ND4L , and ND6 genes have been shown to exhibit Ka/Ks ratios suggesting strong positive selection in certain comparison groups (KT364526 vs. PQ474154, and NC_015526 vs. KU049722) (Table S3).”
Xie, W., Song, K., Klaus, S., et al. (2022) · Avian Research · doi:10.1016/j.avrs.2022.100009 · Cited by 1 · see citing works
Li, Z., Chen, D., & Dong, L. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.01.02.474725
Lamichhaney, S., Palacios, C., Wang, P., Wang, N., Brown, M. M., Capatosto, L., Du, J., Jiang, J., Zhang, Q., & Dahal, N. (2022) · Research Square · doi:10.21203/rs.3.rs-2231100/v1
Эволюционная история курообразных Евразии, "Природа"
Владимирович, З. Н. (2023) · Priroda · doi:10.7868/s0032874x23010027
An almost chromosome-level assembly and annotation of the Alectoris rufa genomePreprint
Eleiwa, A., Nadal, J., Vilaprinyó, E., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.01.11.575009
“Combining those markers with estimates of divergence time gleaned from fossil records and genetic clocks has produced robust phylogenetic trees that can be used to generate strong hypotheses about speciation events 36–38 .”
Владимирович, З. Н. (2024) · Палеонтологический журнал · doi:10.31857/s0031031x24010118
Chapter 1. Comparative Osteology and Phylogeny of Quails and Allies (Coturnicini)
Zelenkov, N. V. (2024) · Paleontological Journal · doi:10.1134/s0031030124600872
“A backbone topology corresponding to the nuclear and mitochondrial phylogenies of galliforms was used as a constraint (Kimball et al., 2021a, 2021b).”
Zelenkov, N. V. (2024) · Палеонтологический журнал · doi:10.31857/s0031031x24030104
Zhao, M., Kimball, R. T., & Braun, E. L. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.02.657453
“In some cases, taxa with poor sequence recovery appear to have exceptionally long terminal branches (e.g., Bernstein and Ruane, 2022; Braun et al., 2024; Derkarabetian et al., 2019; Kimball et al., 2021; McCullough et al., 2024; Nash et al., 2024; Zhao et al., 2025a).”
Self-citationGustafsson, D. R., Li, Z., Tian, C., et al. (2025) · European Journal of Taxonomy · doi:10.5852/ejt.2025.1004.2961
A new Pleistocene peafowl from Taiwan reveals the extinction of a large galliform bird in East Asia
Lan, Y.-J., Mayr, G., & Tsai, C. (2026) · Royal Society Open Science · doi:10.1098/rsos.260347
Yu, T., Li, Z., Stidham, T. A., et al. (2026) · Journal of Paleontology · doi:10.1017/jpa.2026.10229
“However, recent research on Galliformes indicates a closer relationship of Polyplectron to Gallo-perdix , Haematortyx , and Tropicoperdix than to Argusianus , Rheinar-dia , and peafowl (Chen et al., 2021; Kimball et al., 2021).”
Christidis, L., Rheindt, F. E., Iliff, M. J., Lepage, D., Rasmussen, P. C., Donald, P., Alström, P., Areta, J. I., Brammer, F., Chesser, T., et al. (2026) · AviList · doi:10.2173/avilist.v2025b · Cited by 27 · see citing works
How Does the Phasianidae Maintain Its Diversity in Central China?
Li, Q., Su, T., Zha, Y., et al. (2026) · Ecology and Evolution · doi:10.1002/ece3.73796
“This family is divided into 3 subfamilies: Phasianinae, Coturnicinae, and Arborophilinae (Chen et al. 2021; Kimball et al. 2021; Zheng 2015), and is widely distributed across all continents except for Antarctica.”
Painted Francolin (Francolinus pictus)
Madhuhansi, W. K. N. S., Kalukapuge, T., Abegunawardhana, P. D., et al. (2026) · Birds of the World · doi:10.2173/bow.paifra1.01.1
- Authors
- Kimball, R. T., Hosner, P. A., & Braun, E. L.
- Affiliations
- University of Florida (US)
- University of Copenhagen (DK)
- Corresponding author
- Kimball, Rebecca T.
- Venue
- Molecular Phylogenetics and Evolution
- Publisher
- Elsevier BV
- Published
- 2021-05
- Volume
- 158
- Pages
- 107091
- ISSN
- 1055-7903 (ISSN-L)
- OpenAlex
- W3126412472
- Semantic Scholar
- bdb8b62b5a331487f565e3bd337ee10a2cc41323
- Cited by
- 55
- References
- 82
- Citations by year
- 2026: 6 · 2025: 8 · 2024: 23 · 2023: 7 · 2022: 8 · 2021: 3
- FWCI
- 2.76
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- Locations
- Molecular Phylogenetics and Evolution (publishedVersion)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
- Funders
- Danmarks Grundforskningsfond
- Division of Environmental Biology
- Villum Fonden
- 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 › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Diversity and Evolution
- Keywords
- Galliformes, phylogenomics, supermatrix, ultraconserved elements, missing data, macroevolution, chickens, Turkey
- MeSH terms
- Animals, Cell Nucleus, Introns, Mitochondria, Phylogeny, Databases, Genetic, Galliformes
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