Population genomics of parallel hybrid zones in the mimetic butterflies, H. melpomene and H. erato.
Hybrid zones can be valuable tools for studying evolution and identifying genomic regions responsible for adaptive divergence and underlying phenotypic variation. Hybrid zones between subspecies of Heliconius butterflies can be very narrow and are maintained by strong selection acting on color pattern. The comimetic species, H. erato and H. melpomene, have parallel hybrid zones in which both species undergo a change from one color pattern form to another. We use restriction-associated DNA sequencing to obtain several thousand genome-wide sequence markers and use these to analyze patterns of population divergence across two pairs of parallel hybrid zones in Peru and Ecuador. We compare two approaches for analysis of this type of data-alignment to a reference genome and de novo assembly-and find that alignment gives the best results for species both closely (H. melpomene) and distantly (H. erato, ∼15% divergent) related to the reference sequence. Our results confirm that the color pattern controlling loci account for the majority of divergent regions across the genome, but we also detect other divergent regions apparently unlinked to color pattern differences. We also use association mapping to identify previously unmapped color pattern loci, in particular the Ro locus. Finally, we identify a new cryptic population of H. timareta in Ecuador, which occurs at relatively low altitude and is mimetic with H. melpomene malleti.
Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom; Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom;
Nicola J
http://orcid.org/0000-0002-9319-921X
NJ
Nadeau
Department of Biology and Center for Applied Tropical Ecology and Conservation, University of Puerto Rico, Rio Piedras, San Juan, Puerto Rico 00921;
Mayté
M
Ruiz
Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom; Centro de Investigación en Biodiversidad y Cambio Climático (BioCamb), Universidad Tecnológica Indoamérica, Quito, Ecuador;
Patricio
P
Salazar
Department of Biology, Mississippi State University, Mississippi 39762, USA;
Brian
B
Counterman
High Performance Computing Facility, University of Puerto Rico, San Juan, Puerto Rico, 00921;
Jose Alejandro
JA
Medina
High Performance Computing Facility, University of Puerto Rico, San Juan, Puerto Rico, 00921; Department of Computer Science, University of Puerto Rico, Rio Piedras, San Juan, Puerto Rico 00921;
Humberto
H
Ortiz-Zuazaga
Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom;
Anna
A
Morrison
Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancón, Panama.
W Owen
http://orcid.org/0000-0003-2805-2745
WO
McMillan
Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom; Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancón, Panama c.jiggins@zoo.cam.ac.uk.
Chris D
http://orcid.org/0000-0002-7809-062X
CD
Jiggins
Department of Biology and Center for Applied Tropical Ecology and Conservation, University of Puerto Rico, Rio Piedras, San Juan, Puerto Rico 00921;
Riccardo
R
Papa
D000818:Animals; D002080:Butterflies / Q000033:anatomy & histology / Q000235:genetics*; D002874:Chromosome Mapping; D019143:Evolution, Molecular; D056426:Genetic Loci; D049810:Genetic Speciation; D014644:Genetic Variation; D049750:Genome, Insect; D010641:Phenotype; D010802:Phylogeny; D010858:Pigmentation; D014921:Wings, Animal / Q000033:anatomy & histology