Supplementary Figures Figure S1 Population genetic statistics calculated in non-overlapping 10 Kb windows along the 14 chromosomes in the sea squirt genome. Figure S2 C. robusta introgression into C. intestinalis shown across the 14 chromosomes. Figure S3 Population genetic statistics of the C. robusta introgressed coding sequences. Figure S4 ABBA-BABA introgression patterns using C. edwardsi as an outgroup. Figure S5 Inference of the divergence history between C. robusta and C. intestinalis with moments. Figure S6 Selection tests. Figure S7 C. robusta ancestry along chromosome 5 in C. intestinalis individuals. Figure S8 Neighbor-joining trees of 50 Kb windows framing the “missing data region” (grey band) at the center of the chromosome 5 hotspot. Figure S9 Copy number variation at candidate SNPs in the introgression hotspot on chromosome 5 (700 Kb - 1.5 Mb). Figure S10 Structural analysis of the “missing data region” on chromosome 5 (from 1,009,000 to 1,055,000 bp). Supplementary Tables Table S1 Sample information. Table S2 Correlation between chromosomes of the individual C. robusta ancestry fraction. Table S3 Demographic results with moments – excluding chromosome 5. Table S4 Demographic results with moments – including chromosome 5. Table S5 Description of the Supplementary Data. Supplementary Scripts Bioinformatic pipeline used for genotyping and haplotyping. Script #1: prepare the reference genome for BWA and GATK. reference_bwa_GATK_CF.sh Script #2: mapping the reads to the reference with BWA. mapping_bwa-mem_CF.sh Script #3: indel realignment with GATK. indel_realignment_CF.sh Script #4: individual variant calling in gVCF format with GATK. snpindel_callingGVCF_raw_CF.sh Script #5: joint genotyping with GATK. joint_genotyping_raw_CF.sh Script #6: genotype refinement with GATK. genotype_refinement_raw_CF.sh Script #7: SNPs and indels recalibration with GATK. snpindel_recalibration_CF.sh Script #8: genotype refinement after recalibration with GATK. genotype_refinement_recal_CF.sh Script #9: genotype correction. phase_by_transmission_correctCalling_CF@2020.sh Script #10: phasing with GATK and BEAGLE. phase_by_transmission_clean_CF@2020.sh Pipeline used for the demographic inferences with moments. Script #11: define the demographic models. moments_models_2pop_bb_parallel_folded_2periods.py Script #12: run the demographic inferences. moments_inference_dualanneal_bb_parallel_folded_2periods_bounds.py