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Inference of Gene Flow between Species from Genomic Data When the Mode, Direction, and Lineages are Misspecified
Yuttapong Thawornwattana1,2, Tomáš Flouri2, James Mallet1
1Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
Molecular Biology and Evolution
|June 27, 2025
Summary
Genomic data reveals interspecific gene flow shapes biodiversity. Even simplified models like the multispecies coalescent (MSC) effectively infer gene flow, despite potential misspecifications, aiding evolutionary studies.
Area of Science:
- Evolutionary biology
- Genomics
- Biodiversity research
Background:
- Interspecific gene flow is a key driver of biodiversity, increasingly studied using genomic data.
- Multispecies coalescent (MSC) models, including constant-rate migration (MSC-M) and discrete introgression (MSC-I), are used to infer gene flow.
- The simplified nature of these MSC models raises concerns about their accuracy with real-world data.
Purpose of the Study:
- To investigate the inference of gene flow under the MSC-M model.
- To assess the impact of model misspecifications, such as lineage mis-assignment, direction, and mode of gene flow.
- To evaluate the effectiveness of these models using a case study on purple cone spruce (Picea spp.).
Main Methods:
- Theoretical analysis of gene flow inference under the MSC-M model.
- Examination of biases caused by mis-assigning gene flow to incorrect lineages.
- Bayesian testing for inferring recent and ancient gene flow between lineages.
- Analysis of a genomic dataset from Picea spp. to demonstrate practical implications.
Main Results:
- Mis-assigning gene flow to incorrect lineages introduces significant biases in rate estimations.
- Bayesian tests demonstrate high power for detecting both recent and ancient gene flow, even between non-sister lineages.
- Misspecification of the gene flow mode (MSC-I vs. MSC-M) has minor local effects, with gene flow still detectable.
- Despite potential inaccuracies, idealized MSC models, particularly MSC-I, are effective for extracting information on species divergence and gene flow.
Conclusions:
- Simplified MSC models are powerful tools for inferring gene flow and species divergence from genomic data.
- Understanding and accounting for model misspecifications are crucial for accurate gene flow inference.
- The study highlights the utility of MSC models, even with their idealized assumptions, in evolutionary research.
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