Can’t see the forest for the trees: The influence of marker type on inferred phylogenetic relationships in a cosmopolitan bat genus
Abstract
Fine-resolution information on species relationships and biological diversity is critically needed to guide conservation efforts amidst rapid environmental changes. Systematics, which forms the foundation of this knowledge, has been revolutionized by phylogenomics, utilizing genome-scale datasets. However, the use of diverse marker types, non-comparable taxon sampling, and outgroup selection can lead to conflicting phylogenetic hypotheses. These inconsistencies complicate study comparisons and hinder our ability to assess marker-specific impacts on phylogenetic resolution. The phylogenetic reconstruction of the bat genus Myotis, encompassing over 140 species and characterized by a rapid radiation in the last 20 million years, has been particularly influenced by these challenges. Achieving phylogenetic resolution in Myotis is particularly complex due to subtle interspecific differences in both morphological and molecular traits. Mitochondrial and nuclear markers often produce discordant trees, influenced by hybridization, introgression, and methodological variations. In this study, we employed a consistent taxonomic sample set of 44 Myotis taxa to evaluate the impact of five different genetic marker types on phylogenetic reconstruction. We observed significant discordance between topologies derived from conserved nuclear and mitochondrial markers and found that transposable elements were inadequate for resolving relationships across the entire genus. Our results also clarify the placement of previously problematic taxa within the genus. These findings emphasize the importance of aligning genetic marker choice with specific phylogenetic questions and highlight the influence of taxonomic and methodological variation on phylogenomic outcomes. This work provides a framework for improving phylogenetic inference in rapidly radiating groups and enhances our understanding of evolutionary history in Myotis.
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BibTeX
@article{lilley2026cant,
title = {{Can’t see the forest for the trees: The influence of marker type on inferred phylogenetic relationships in a cosmopolitan bat genus}},
author = {Thomas Lilley and Veronika Laine and Fernanda Ito dos Santos and Flora Whiting-Fawcett and Diego Porto and Aída Otálora-Ardila and Enrico Bernard and Michael Buchalski and Devaughn Fraser and Joseph Hoyt and Joseph Johnson and Kuniko Kawai and Gonzalo Ossa and Steve Paterson and Sébastien Puechmaille and Attila Sándor and Aliaksei Shpak and Dmitriy Smirnov and Niklas Wahlberg and Victoria Twort},
journal = {Molecular Phylogenetics and Evolution},
year = {2026},
month = aug,
doi = {10.1016/j.ympev.2026.108719},
url = {https://hal.science/hal-05783406v1},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Can’t see the forest for the trees: The influence of marker type on inferred phylogenetic relationships in a cosmopolitan bat genus
AU - Thomas Lilley
AU - Veronika Laine
AU - Fernanda Ito dos Santos
AU - Flora Whiting-Fawcett
AU - Diego Porto
AU - Aída Otálora-Ardila
AU - Enrico Bernard
AU - Michael Buchalski
AU - Devaughn Fraser
AU - Joseph Hoyt
AU - Joseph Johnson
AU - Kuniko Kawai
AU - Gonzalo Ossa
AU - Steve Paterson
AU - Sébastien Puechmaille
AU - Attila Sándor
AU - Aliaksei Shpak
AU - Dmitriy Smirnov
AU - Niklas Wahlberg
AU - Victoria Twort
PY - 2026
DA - 2026/08/13
JO - Molecular Phylogenetics and Evolution
DO - 10.1016/j.ympev.2026.108719
UR - https://hal.science/hal-05783406v1
AB - Fine-resolution information on species relationships and biological diversity is critically needed to guide conservation efforts amidst rapid environmental changes. Systematics, which forms the foundation of this knowledge, has been revolutionized by phylogenomics, utilizing genome-scale datasets. However, the use of diverse marker types, non-comparable taxon sampling, and outgroup selection can lead to conflicting phylogenetic hypotheses. These inconsistencies complicate study comparisons and hinder our ability to assess marker-specific impacts on phylogenetic resolution. The phylogenetic reconstruction of the bat genus Myotis, encompassing over 140 species and characterized by a rapid radiation in the last 20 million years, has been particularly influenced by these challenges. Achieving phylogenetic resolution in Myotis is particularly complex due to subtle interspecific differences in both morphological and molecular traits. Mitochondrial and nuclear markers often produce discordant trees, influenced by hybridization, introgression, and methodological variations. In this study, we employed a consistent taxonomic sample set of 44 Myotis taxa to evaluate the impact of five different genetic marker types on phylogenetic reconstruction. We observed significant discordance between topologies derived from conserved nuclear and mitochondrial markers and found that transposable elements were inadequate for resolving relationships across the entire genus. Our results also clarify the placement of previously problematic taxa within the genus. These findings emphasize the importance of aligning genetic marker choice with specific phylogenetic questions and highlight the influence of taxonomic and methodological variation on phylogenomic outcomes. This work provides a framework for improving phylogenetic inference in rapidly radiating groups and enhances our understanding of evolutionary history in Myotis.
SN - 1055-7903
SN - 1095-9513
ER -