TY - JOUR
T1 - Inferring introgression using RADseq and DFOIL
T2 - Power and pitfalls revealed in a case study of spiny lizards (Sceloporus)
AU - Lambert, Shea M.
AU - Streicher, Jeffrey W.
AU - Fisher-Reid, M. Caitlin
AU - Méndez de la Cruz, Fausto R.
AU - Martínez-Méndez, Norberto
AU - García-Vázquez, Uri Omar
AU - Nieto Montes de Oca, Adrián
AU - Wiens, John J.
N1 - Funding Information:
National Science Foundation, Grant/Award Number: 2012117663, 1655690; Society for the Study of Evolution; Society of Systematic Biologists
Funding Information:
We thank Harsimran Brar, Liz Miller and Tereza Jezkova for help in the laboratory, and Anthony Baniaga, Tim O'Connor and Tod W. Reeder for help in the field. We thank Nicholas Barton and an anonymous reviewer for helpful comments that improved the manuscript. We thank Kathryn Chenard for the artwork of S. oberon and S. ornatus in Figures 2, 3 and 4. This work was partially funded by awards from the Society for the Study of Evolution (Rosemary Grant Award) and Society of Systematic Biologists (Graduate Student Research Award) to SML. This material is based upon work supported by the U.S. National Science Foundation, including a Graduate Research Fellowship to SML (Grant No. 2012117663) and NSF DEB 1655690 to JJW. Any opinion, findings, and conclusions or recommendations expressed in this material are those of the authors(s) and do not necessarily reflect the views of the National Science Foundation.
Publisher Copyright:
© 2018 John Wiley & Sons Ltd
PY - 2019/7
Y1 - 2019/7
N2 - Introgression is now commonly reported in studies across the Tree of Life, aided by recent advancements in data collection and analysis. Nevertheless, researchers working with nonmodel species lacking reference genomes may be stymied by a mismatch between available resources and methodological demands. In this study, we demonstrate a fast and simple approach for inferring introgression using RADseq data, and apply it to a case study involving spiny lizards (Sceloporus) from northeastern México. First, we find evidence for recurrent mtDNA introgression between the two focal species based on patterns of mito-nuclear discordance. We then test for nuclear introgression by exhaustively applying the “five-taxon” D-statistic (DFOIL) to all relevant individuals sampled for RADseq data. In our case, this exhaustive approach (dubbed “ExDFOIL”) entails testing up to ~250,000 unique four-taxon combinations of individuals across species. To facilitate use of this ExDFOIL approach, we provide scripts for many relevant tasks, including the selection of appropriate four-taxon combinations, execution of DFOILtests in parallel and visualization of introgression results in phylogenetic and geographic space. Using ExDFOIL, we find evidence for ancient introgression between the focal species. Furthermore, we reveal geographic variation in patterns of introgression that is consistent with patterns of mito-nuclear discordance and with recurrent introgression. Overall, our study demonstrates that the combination of DFOIL and RADseq data can effectively detect introgression under a variety of sampling conditions (for individuals, populations and loci). Importantly, we also find evidence that batch-specific error and linkage in RADseq data may mislead inferences of introgression under certain conditions.
AB - Introgression is now commonly reported in studies across the Tree of Life, aided by recent advancements in data collection and analysis. Nevertheless, researchers working with nonmodel species lacking reference genomes may be stymied by a mismatch between available resources and methodological demands. In this study, we demonstrate a fast and simple approach for inferring introgression using RADseq data, and apply it to a case study involving spiny lizards (Sceloporus) from northeastern México. First, we find evidence for recurrent mtDNA introgression between the two focal species based on patterns of mito-nuclear discordance. We then test for nuclear introgression by exhaustively applying the “five-taxon” D-statistic (DFOIL) to all relevant individuals sampled for RADseq data. In our case, this exhaustive approach (dubbed “ExDFOIL”) entails testing up to ~250,000 unique four-taxon combinations of individuals across species. To facilitate use of this ExDFOIL approach, we provide scripts for many relevant tasks, including the selection of appropriate four-taxon combinations, execution of DFOILtests in parallel and visualization of introgression results in phylogenetic and geographic space. Using ExDFOIL, we find evidence for ancient introgression between the focal species. Furthermore, we reveal geographic variation in patterns of introgression that is consistent with patterns of mito-nuclear discordance and with recurrent introgression. Overall, our study demonstrates that the combination of DFOIL and RADseq data can effectively detect introgression under a variety of sampling conditions (for individuals, populations and loci). Importantly, we also find evidence that batch-specific error and linkage in RADseq data may mislead inferences of introgression under certain conditions.
KW - ABBA-BABA
KW - D-statistics
KW - batch effects
KW - hybridization
KW - mito-nuclear discordance
UR - http://www.scopus.com/inward/record.url?scp=85065340022&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85065340022&partnerID=8YFLogxK
U2 - 10.1111/1755-0998.12972
DO - 10.1111/1755-0998.12972
M3 - Article
C2 - 30506631
AN - SCOPUS:85065340022
SN - 1755-098X
VL - 19
SP - 818
EP - 837
JO - Molecular Ecology Resources
JF - Molecular Ecology Resources
IS - 4
ER -