Contradictory Phylogenetic Signals in the Laurasiatheria Anomaly Zone

Doronina, Liliya; Hughes, Graham M.; Moreno-Santillan, Diana; Lawless, Colleen; Lonergan, Tadhg; Ryan, Louise; Jebb, David; Kirilenko, Bogdan M.; Korstian, Jennifer M.; Dávalos, Liliana M.; Vernes, Sonja C.; Myers, Eugene W.; Teeling, Emma C.; Hiller, Michael; Jermiin, Lars S.; Schmitz, Jürgen; Springer, Mark S.; Ray, David A.

doi:10.3390/genes13050766

Open AccessArticle

Contradictory Phylogenetic Signals in the Laurasiatheria Anomaly Zone

by

Liliya Doronina

^1,*,†

,

Graham M. Hughes

^2,*,†

,

Diana Moreno-Santillan

^3,4,

Colleen Lawless

²

,

Tadhg Lonergan

²

,

Louise Ryan

²

,

David Jebb

^5,6,7,

Bogdan M. Kirilenko

^8,9,10,

Jennifer M. Korstian

³,

Liliana M. Dávalos

¹¹,

Sonja C. Vernes

^12,13,

Eugene W. Myers

^5,14,15,

Emma C. Teeling

²,

Michael Hiller

^8,9,10

,

Lars S. Jermiin

^2,16,17,

Jürgen Schmitz

¹

,

Mark S. Springer

¹⁸ and

David A. Ray

^3,*

¹

Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany

²

School of Biology and Environmental Science, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland

³

Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA

⁴

Department of Integrative Biology, University of California, Berkeley, CA 92697, USA

⁵

Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany

⁶

Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany

⁷

Center for Systems Biology Dresden, 01307 Dresden, Germany

⁸

LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany

⁹

Senckenberg Research Institute, 60325 Frankfurt, Germany

¹⁰

Faculty of Biosciences, Goethe-University, 60438 Frankfurt, Germany

¹¹

Department of Ecology and Evolution and Consortium for Inter—Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY 11794, USA

¹²

School of Biology, The University of St Andrews, St Andrews KY16 9ST, UK

¹³

Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, 6525 Nijmegen, The Netherlands

¹⁴

Faculty of Computer Science, Technical University Dresden, 01307 Dresden, Germany

¹⁵

The Okinawa Institute of Science and Technology, Okinawa 904-0495, Japan

¹⁶

Research School of Biology, Australian National University, Canberra, ACT 2601, Australia

¹⁷

Earth Institute, University College Dublin, D04 V1W8 Dublin, Ireland

¹⁸

Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, CA 92521, USA

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^*

Authors to whom correspondence should be addressed.

^†

These authors contributed equally to this work.

Genes 2022, 13(5), 766; https://doi.org/10.3390/genes13050766

Submission received: 29 March 2022 / Revised: 12 April 2022 / Accepted: 21 April 2022 / Published: 26 April 2022

(This article belongs to the Special Issue Mobile Elements in Phylogenomic Reconstructions)

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Abstract

Relationships among laurasiatherian clades represent one of the most highly disputed topics in mammalian phylogeny. In this study, we attempt to disentangle laurasiatherian interordinal relationships using two independent genome-level approaches: (1) quantifying retrotransposon presence/absence patterns, and (2) comparisons of exon datasets at the levels of nucleotides and amino acids. The two approaches revealed contradictory phylogenetic signals, possibly due to a high level of ancestral incomplete lineage sorting. The positions of Eulipotyphla and Chiroptera as the first and second earliest divergences were consistent across the approaches. However, the phylogenetic relationships of Perissodactyla, Cetartiodactyla, and Ferae, were contradictory. While retrotransposon insertion analyses suggest a clade with Cetartiodactyla and Ferae, the exon dataset favoured Cetartiodactyla and Perissodactyla. Future analyses of hitherto unsampled laurasiatherian lineages and synergistic analyses of retrotransposon insertions, exon and conserved intron/intergenic sequences might unravel the conflicting patterns of relationships in this major mammalian clade.

Keywords: retrophylogenomics; exon concatenation; exon coalescence; Laurasiatheria; Scrotifera; anomaly zone

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MDPI and ACS Style

Doronina, L.; Hughes, G.M.; Moreno-Santillan, D.; Lawless, C.; Lonergan, T.; Ryan, L.; Jebb, D.; Kirilenko, B.M.; Korstian, J.M.; Dávalos, L.M.; et al. Contradictory Phylogenetic Signals in the Laurasiatheria Anomaly Zone. Genes 2022, 13, 766. https://doi.org/10.3390/genes13050766

AMA Style

Doronina L, Hughes GM, Moreno-Santillan D, Lawless C, Lonergan T, Ryan L, Jebb D, Kirilenko BM, Korstian JM, Dávalos LM, et al. Contradictory Phylogenetic Signals in the Laurasiatheria Anomaly Zone. Genes. 2022; 13(5):766. https://doi.org/10.3390/genes13050766

Chicago/Turabian Style

Doronina, Liliya, Graham M. Hughes, Diana Moreno-Santillan, Colleen Lawless, Tadhg Lonergan, Louise Ryan, David Jebb, Bogdan M. Kirilenko, Jennifer M. Korstian, Liliana M. Dávalos, and et al. 2022. "Contradictory Phylogenetic Signals in the Laurasiatheria Anomaly Zone" Genes 13, no. 5: 766. https://doi.org/10.3390/genes13050766

APA Style

Doronina, L., Hughes, G. M., Moreno-Santillan, D., Lawless, C., Lonergan, T., Ryan, L., Jebb, D., Kirilenko, B. M., Korstian, J. M., Dávalos, L. M., Vernes, S. C., Myers, E. W., Teeling, E. C., Hiller, M., Jermiin, L. S., Schmitz, J., Springer, M. S., & Ray, D. A. (2022). Contradictory Phylogenetic Signals in the Laurasiatheria Anomaly Zone. Genes, 13(5), 766. https://doi.org/10.3390/genes13050766

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Contradictory Phylogenetic Signals in the Laurasiatheria Anomaly Zone

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