DOI: 10.5061/dryad.bcc2fqz91
title: Data from: Contrasting signatures of genomic divergence during sympatric speciation

description: The transition from “well-marked varieties” into “well-defined species”
 has puzzled evolutionary biologists ever since Darwin —
 especially when extensive gene flow between incipient species is possible
 due to the lack of physical barriers (sympatric speciation). Gene flow
 counteracts the build-up of genome-wide differentiation, which is both a
 hallmark of speciation and forms the underlying basis of irreversible
 reproductive barriers (incompatibilities) that ultimately complete the
 speciation process. Theory predicts that the genetic architecture of
 divergently selected traits can influence whether sympatric speciation
 occurs. However, empirical data to test this prediction remain rare and
 are often difficult to synthesize across animal taxa due to idiosyncrasies
 in their biology and evolutionary histories. Here, within a young species
 complex of Neotropical cichlid fish (Amphilophus spp.), we analyzed
 genomic divergence among populations and species, and the genetic
 architecture of traits that have been suggested to be important for this
 divergence, by generating a new genome assembly and re-sequencing 453
 genomes. We found that species differing in mono/oligogenic traits
 affecting ecological performance and/or mate choice show remarkably
 localized genomic differentiation. In contrast, differentiation between
 species that diverged in polygenic traits is widespread and much higher
 overall, consistent with the evolution of effective and stable genome-wide
 barriers to gene flow. Thus, we conclude that simple trait architectures
 are not always as conducive to speciation-with-gene-flow as previously
 suggested, whereas, unexpectedly, polygenic architectures can promote
 rapid and stable speciation in sympatry.
description: This work is based on a new, high-quality reference genome of
 Amphilophus citrinellus and 453 re-sequenced genomes that were sampled
 between 2003 and 2015. Sample sizes for the resequenced genomes (in [])
 are GL Nicaragua A. citrinellus [24], GL Nicaragua A. labiatus [24], GL
 Managua A. citrinellus [25], GL Managua A. labiatus [25], CL Apoyeque A.
 cf. citrinellus [40], CL Apoyo A. astorquii [23], CL Apoyo A. chancho
 [16], CL Apoyo A. flaveolus [16], CL Apoyo A. globosus [25], CL Apoyo A.
 supercilius [10], CL Apoyo A. zaliosus [21], CL Apoyo admixed individuals
 [9], CL As. León A. cf. citrinellus [20], CL As. Managua A. tolteca [20],
 CL Xiloá A. amarillo [21], CL Xiloá A. sagittae [27], CL Xiloá A. viridis
 [24], CL Xiloá A. xiloaensis [16], CL Xiloá admixed individuals [14], CL
 Masaya A. cf. citrinellus [40], CL Tiscapa A. cf. citrinellus [20]. Fish
 were caught with gill nets or by harpooning in crater lakes Asososca León,
 Asososca Managua, Apoyeque, Apoyo, Masaya Tiscapa, and Xiloá. Fish or
 tissue samples from the great lakes Nicaragua and Managua were obtained
  from local fishermen, mostly the big fish market in Granada (Lake
 Nicaragua fish) and Mateares (Lake Managua fish). Adult fish were
 collected in field expeditions of the Meyer lab to Nicaragua between 2003
 and 2015. Photographs were taken in the field. Next-generation sequencing
 data generation was performed at the University of Konstanz, the Max
 Planck Institute of Molecular Cell Biology and Genetics in Dresden, and
 BGI Hongkong.