16While speciation underlies novel biodiversity, it is poorly understood how natural 17 selection shapes genomes during speciation. Selection is assumed to act against gene 18 flow at barrier loci, promoting reproductive isolation and speciation. However, 19 evidence for gene flow and selection is often indirect. Here we utilize haplodiploidy 20 to identify candidate barrier loci in hybrids between two wood ant species and 21 integrate survival analysis to directly measure if natural selection is acting at 22 candidate barrier loci. We find multiple candidate barrier loci but surprisingly, 23 proportion of them show leakage between samples collected ten years apart, natural 24 selection favoring leakage in the latest sample. Barrier leakage and natural selection 25 for introgressed alleles could be due to environment-dependent selection, 26 emphasizing the need to consider temporal variation in natural selection in future 27 speciation work. Integrating data on survival allows us to move beyond genome 28 scans, demonstrating natural selection acting on hybrid genomes in real-time. 29 30 New species are formed when populations become reproductively isolated, i.e. they 68 do not interbreed and exchange genetic material [1]. However, until complete 69 reproductive isolation has evolved gene flow may still occur between the diverging 70 lineages. This genetic exchange is usually localized in the genome, with some regions 71 of the genome resisting gene flow better than others. Regions resistant to gene flow 72 are thought to harbor "barrier loci" that can drive the divergence between lineages 73 despite the homogenizing effect of gene flow [2]. Barrier loci could contribute to 74 reproductive isolation by allowing differential adaptation between diverging lineages 75 [2]. Alternatively, barrier loci could consist of genes incompatible between the 76 diverging lineages (Dobzhansky-Muller incompatibilities [3,4], DMIs) driven by drift 77 or divergent selection [5]. 78 79 Several recent studies have searched for barrier loci using genome scans and 80 identified genomic islands of differentiation using various measures of genetic 81 differentiation [e.g. refs 6-8]. The underlying assumption in these genome scans is 82 that the most differentiated genomic regions between hybridizing lineages are those 83 that are resistant to gene flow and hence drive reproductive isolation. Genetic 84 differentiation however is an indirect measure of gene flow and several problems with 85 genome scans have been discussed [e.g. refs 9, 10]. The main problem lies in the fact 86 that several other evolutionary forces (such as low recombination rate or drift) can 87 bring about genomic regions of seemingly high differentiation between populations. 88Thus, we need more studies that test if natural selection is promoting speciation and 89 halting gene flow at these genomic regions in natural populations. 90 91 Here we use ants as a model system to discover genomic regions of divergence (i.e. 92 putative barrier loci) and to test for natural se...