DOI: 10.5061/dryad.m1572
title: Data from: Semi-permeable species boundaries in Iberian barbels (Barbus and Luciobarbus, Cyprinidae)

description: Background: The evolution of species boundaries and the relative impact of
 selection and gene flow on genomic divergence are best studied in
 populations and species pairs exhibiting various levels of divergence
 along the speciation continuum. We studied species boundaries in Iberian
 barbels, Barbus and Luciobarbus, a system of populations and species
 spanning a wide degree of genetic relatedness, as well as geographic
 distribution and range overlap. We jointly analyze multiple types of
 molecular markers and morphological traits to gain a comprehensive
 perspective on the nature of species boundaries in these cyprinid fishes.
 Results: Intraspecific molecular and morphological differentiation is
 visible among many populations. Genomes of all sympatric species studied
 are porous to gene flow, even if they are not sister species. Compared to
 their allopatric counterparts, sympatric representatives of different
 species share alleles and show an increase in all measures of nucleotide
 polymorphism (S, H d, K, π and θ). High molecular diversity is
 particularly striking in L. steindachneri from the Tejo and Guadiana
 rivers, which co-varies with other sympatric species. Interestingly,
 different nuclear markers introgress across species boundaries at various
 levels, with distinct impacts on population trees. As such, some loci
 exhibit limited introgression and population trees resemble the presumed
 species tree, while alleles at other loci introgress more freely and
 population trees reflect geographic affinities and interspecific gene
 flow. Additionally, extent of introgression decreases with increasing
 genetic divergence in hybridizing species pairs. Conclusions: We show that
 reproductive isolation in Iberian Barbus and Luciobarbus is not complete
 and species boundaries are semi-permeable to (some) gene flow, as
 different species (including non-sister) are exchanging genes in areas of
 sympatry. Our results support a speciation-with-gene-flow scenario with
 heterogeneous barriers to gene flow across the genome, strengthening with
 genetic divergence. This is consistent with observations coming from other
 systems and supports the notion that speciation is not instantaneous but a
 gradual process, during which different species are still able to exchange
 some genes, while selection prevents gene flow at other loci. We also
 provide evidence for a hybrid origin of a barbel ecotype, L.
 steindachneri, suggesting that ecology plays a key role in species
 coexistence and hybridization in Iberian barbels. This ecotype with
 intermediate, yet variable, molecular, morphological, trophic and
 ecological characteristics is the local product of introgressive
 hybridization of L. comizo with up to three different species (with L.
 bocagei in the Tejo, with L. microcephalus and L. sclateri in the
 Guadiana). In spite of the homogenizing effects of ongoing gene flow,
 species can still be discriminated using a combination of morphological
 and molecular markers. Iberian barbels are thus an ideal system for the
 study of species boundaries, since they span a wide range of genetic
 divergences, with diverse ecologies and degrees of sympatry.
description: GH-1_PhasedGrowth hormone-1 sequence data, phasedGH-2_PhasedGrowth hormone-2 sequence data, phasedS7-1_PhasedS7-1 sequence data, phasedS7-2_PhasedS7-2 sequence data, phasedMtDNACytochrome b sequence dataMeristicsMeristic data