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Open Access Open Badges Research article

Timing major conflict between mitochondrial and nuclear genes in species relationships of Polygonia butterflies (Nymphalidae: Nymphalini)

Niklas Wahlberg1*, Elisabet Weingartner2, Andrew D Warren34 and Sören Nylin2

Author Affiliations

1 Laboratory of Genetics, Department of Biology, University of Turku, 20014 Turku, Finland

2 Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden

3 McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, SW 34th Street and Hull Road, PO Box 112710, Gainesville, FL 32611-2710, USA

4 Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Apdo. Postal 70-399, México, DF 04510 México

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BMC Evolutionary Biology 2009, 9:92  doi:10.1186/1471-2148-9-92

Published: 7 May 2009



Major conflict between mitochondrial and nuclear genes in estimating species relationships is an increasingly common finding in animals. Usually this is attributed to incomplete lineage sorting, but recently the possibility has been raised that hybridization is important in generating such phylogenetic patterns. Just how widespread ancient and/or recent hybridization is in animals and how it affects estimates of species relationships is still not well-known.


We investigate the species relationships and their evolutionary history over time in the genus Polygonia using DNA sequences from two mitochondrial gene regions (COI and ND1, total 1931 bp) and four nuclear gene regions (EF-1α, wingless, GAPDH and RpS5, total 2948 bp). We found clear, strongly supported conflict between mitochondrial and nuclear DNA sequences in estimating species relationships in the genus Polygonia. Nodes at which there was no conflict tended to have diverged at the same time when analyzed separately, while nodes at which conflict was present diverged at different times. We find that two species create most of the conflict, and attribute the conflict found in Polygonia satyrus to ancient hybridization and conflict found in Polygonia oreas to recent or ongoing hybridization. In both examples, the nuclear gene regions tended to give the phylogenetic relationships of the species supported by morphology and biology.


Studies inferring species-level relationships using molecular data should never be based on a single locus. Here we show that the phylogenetic hypothesis generated using mitochondrial DNA gives a very different interpretation of the evolutionary history of Polygonia species compared to that generated from nuclear DNA. We show that possible cases of hybridization in Polygonia are not limited to sister species, but may be inferred further back in time. Furthermore, we provide more evidence that Haldane's effect might not be as strong a process in preventing hybridization in butterflies as has been previously thought.