DOI: 10.5061/dryad.8673j
title: Data from: When homoplasy mimics hybridization: a case study of Cape hakes (Merluccius capensis and M. paradoxus)

description: In the marine environment, an increasing number of studies have documented
 introgression and hybridization using genetic markers. Hybridization
 appears to occur preferentially between sister-species, with the
 probability of introgression decreasing with an increase in evolutionary
 divergence. Exceptions to this pattern were reported for the Cape hakes
 (Merluccius capensis and M. paradoxus), two distantly related Merluciidae
 species that diverged 3–4.2 million years ago. Yet, it is expected that
 contemporary hybridization between such divergent species would result in
 reduced hybrid fitness. We analysed 1,137 hake individuals using nine
 microsatellite markers and control region mtDNA data to assess the
 validity of the described hybridization event. To distinguish between
 interbreeding, ancestral polymorphism and homplasy we sequenced the
 flanking region of the most divergent microsatellite marker. Simulation
 and empirical analyses showed that hybrid identification significantly
 varied with the number of markers, model and approach used. Phylogenetic
 analyses based on the sequences of the flanking region of Mmerhk-3b,
 combined with the absence of mito-nuclear discordance, suggest that
 previously reported hybridization between M. paradoxus and M. capensis
 cannot be substantiated. Our findings highlight the need to conduct a
 priori simulation studies to establish the suitability of a particular set
 of microsatellite loci for detecting multiple hybridization events. In our
 example, the identification of hybrids was severely influenced by the
 number of loci and their variability, as well as the different models
 employed. More importantly, we provide quantifiable evidence showing that
 homoplasy mimics the effects of heterospecific crossings which can lead to
 the incorrect identification of hybridization. In the marine environment,
 an increasing number of studies have documented introgression and
 hybridization using genetic markers. Hybridization appears to occur
 preferentially between sister-species, with the probability of
 introgression decreasing with an increase in evolutionary divergence.
 Exceptions to this pattern were reported for the Cape hakes (Merluccius
 capensis and M. paradoxus), two distantly related Merluciidae species that
 diverged 3–4.2 million years ago. Yet, it is expected that contemporary
 hybridization between such divergent species would result in reduced
 hybrid fitness. We analysed 1,137 hake individuals using nine
 microsatellite markers and control region mtDNA data to assess the
 validity of the described hybridization event. To distinguish between
 interbreeding, ancestral polymorphism and homplasy we sequenced the
 flanking region of the most divergent microsatellite marker. Simulation
 and empirical analyses showed that hybrid identification significantly
 varied with the number of markers, model and approach used. Phylogenetic
 analyses based on the sequences of the flanking region of Mmerhk-3b,
 combined with the absence of mito-nuclear discordance, suggest that
 previously reported hybridization between M. paradoxus and M. capensis
 cannot be substantiated. Our findings highlight the need to conduct a
 priori simulation studies to establish the suitability of a particular set
 of microsatellite loci for detecting multiple hybridization events. In our
 example, the identification of hybrids was severely influenced by the
 number of loci and their variability, as well as the different models
 employed. More importantly, we provide quantifiable evidence showing that
 homoplasy mimics the effects of heterospecific crossings which can lead to
 the incorrect identification of hybridization.
description: Henriques et al:
 microsatellite databaseMicrosatellite allelic
 scoring for M. capensis and M. paradoxusHenriques et
 al-database.txt