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Molecular evidence for introgressive hybridization in New Zealand masked gulls

Genetic data and codes to reproduce the analyses from the manuscript : Given, A. D., Mills, J. A., Momigliano, P., & Baker, A. J. (2022). Molecular evidence for introgressive hybridization in New Zealand masked gulls. Ibis. https://doi.org/10.1111/ibi.13117 The data and codes are  in  two zipped folders <ol> <li>FSC.zip</li> <li>PopGen.zip</li> </ol> The FSC.zip folder contains data and scripts to reproduce the fastsimcoal simulations and to calculate summary statistics from observed and simulated data. It also includes the results from these analyses and an R script to run ABC model selection via random forest.   The PopGen.zip folder contains the microsatellite dataset in both genepop (RB-BB.gen) and structure (RB-BB.str) formats , the results from STRUCTURE analyses (folder RB-BB_STRUCT), and an R script (Popgen_analyses.r) to reproduce population genetic analyses (PCA and summary statistics: FST, and estimate HWE,  HO and HE) and plots.

opencc-by-4.0Aug 2022View details →

Supplementary Data of "Introgression between highly divergent sea squirt genomes: an adaptive breakthrough?"

Datasets used in the analyses (see Table S5 for a detailed description). ► Dataset #1: phased SNPs with offspring. joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_phased_phasedBeagle.vcf ► Dataset #2: all SNPs with missing data. joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_parents_oNA5.vcf ► Dataset #3a: phased SNPs. joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_phased_phasedBeagle_parents.vcf ► Dataset #3b: CDS version of “phased SNPs”. joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_phased_phasedBeagle_parents_SNP_CHRall.orf.cds ► Dataset #3c: FASTA version of “phased SNPs”. joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_phased_phasedBeagle_parents_SNP_chr5.sub_${START}-${END}.fasta ► Dataset #4: ancestry informative phased SNPs. joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_phased_phasedBeagle_parents.frq.fixed.vcf ► Dataset #5: all SNPs. joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_parents_oNA.vcf ► Dataset #6: all polarized SNPs. joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_parents_raw_refine_HQ_edwardsi_oNA3_polar.vcf ► Dataset #7: unfiltered mapping files. ciona_bwa-mapping_${IND}_bwa_mem_mdup_IR_chromosome5:700000-1500000_sorted_nodup.bam

opencc-by-4.0Aug 2022View details →

Supplementary Information of "Introgression between highly divergent sea squirt genomes: an adaptive breakthrough?"

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

Fig. 11 in Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations

Fig. 11 Rates of chatter calls in different magpie populations and individuals. a Each mark represents average chattering rate for a single bird from five populations indicated by colours. Figures are numbers for the outliers: 1, 2—jankowskii from the mixed population of Argun'; 3, 4, 5—hybrid birds from the hybridogeneous population of Kerulen. b Each mark represents average chattering rate for a series of chatterings of one selected individual representing jankowskii, leucoptera, and hybrid birds, respectively. Green mark—pair #6 jankowskii from Vladivostok; gray—pair #43 leucoptera from Tsasuchei, Transbaikalia; blue—pair #24 hybrids from Kerulen, eastern Mongolia. X-axis—number of elements per second in a total series of chattering; Y-axis— number of elements per second in a series of 5 elements of chattering

Fig. 12 in Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations

Fig. 12 Violin plot diagram of the chatter call speed (elements per second) of Eurasian magpie populations across regions. X-axis presents a set of populations; Y-axis—elements per second. Box outlines the interquantile range (25%, 75%), whiskers represent range without outliers, central bar is the median, red dot is the mean, and figure shape is the probability density. The brackets on the top denote statistically significant pairwise differences (GamesHowell test, p<0.05)

Fig. 9 in Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations

Fig. 9 Population genetic structure based on unlinked SNP markers. Scatter plots of principal component analysis (PCA) show individual variation in components one and two (a) and three and four (b). The amount of variance explained by each PC is shown in parentheses. I—leucoptera,

Fig. 7 in Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations

Fig. 7 Bayesian skyline plots (BSPs) for effective female population sizes for haplogroups, subspecies, and populations of Pica pica. a Comparison of 6 haplogroups, depicted in the network Fig. 4. b Comparison of 6 subspecies. c Comparison of 4 populations of P. p. jankowskii. d Comparison of 3 populations of P. p. leucoptera.

Fig. 6 in Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations

Fig. 6 Mismatch distribution of nucleotide differences in populations representing different haplogroups as at Figs. 4 and 5. X-axis— number of nucleotide differences; Y-axis—proportion (frequency). Solid lines—expected distributions (under expectation of population growth); dashed lines—observed distributions. a Haplogroup 1:

Fig. 5 in Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations

Fig. 5 Time-calibrated Bayesian tree based on mitochondrial control region sequences of Pica pica. Numbers at the branches indicate Bayesian posterior probability values (left) and bootstrap values of the ML analysis (right, in percent). Triangle widths are proportional to specimen numbers. Blue bars next to nodes indicate 95% credibility intervals for their age estimates. The figures in bold and the time scale below are in million years (Ma) before present

Fig. 4 in Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations

Fig. 4 Phylogenetic medianjoining network based on 256 mitochondrial control region sequences. Sizes of circles correspond to the number of birds sharing this haplotype; branch lengths are proportional to the number of substitutions and those over 2 are shown at the branches. Haplogroups 1–6 are indicated by numbers

Fig. 2 in Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations

Fig. 2 Map of sampling localities for mitochondrial DNA analysis in the zone of contact between Pica pica leucoptera and Pica pica jankowskii. Distribution of haplotypes is indicated by colours: Pica

Fig. 1 in Morphological characters and SNP markers suggest hybridization and introgression in sympatric populations of the pleurocarpous mosses Homalothecium lutescens and H. sericeum

Fig. 1 Measurements of branch leaf characteristics of Homalothecium spp. Leaf characters (L1-L18) are explained in Table 3

Fig. 4 in Morphological characters and SNP markers suggest hybridization and introgression in sympatric populations of the pleurocarpous mosses Homalothecium lutescens and H. sericeum

Fig. 4 Relationship between width and length of leaf lamina of Homalothecium leaf specimens (N = 240) collected from the allopatric populations of H. lutescens (N = 60) and H. sericeum (N = 59) and the

Fig. 6 in Morphological characters and SNP markers suggest hybridization and introgression in sympatric populations of the pleurocarpous mosses Homalothecium lutescens and H. sericeum

Fig. 6 The positions of putatively hybrid sporophytes from the sympatric populations of H. lutescens and H. sericeum superimposed in the PCA from Fig. 5, based on leaf morphology of the maternal gametophytes. The morphospace of leaves from allopatric populations of H. lutescens and H. sericeum are shown as encircled surfaces (blue circle = H. lutescens and yellow circle = H. sericeum). The red circle represents the morphospace of individuals from the sympatric populations. Each square represents a hybrid sporophyte specimen, collected on its

Fig. 5 in Morphological characters and SNP markers suggest hybridization and introgression in sympatric populations of the pleurocarpous mosses Homalothecium lutescens and H. sericeum

Fig. 5 Principal component analysis of 14 leaf characters from 240 specimens representing allopatric and sympatric populations of Homalothecium lutescens and H. sericeum. The first two axes (PC1 and PC2) representing together 36% of variation are shown. The colours and shapes of data points correspond to the population of the specimens. Leaf

Fig. 2 in Morphological characters and SNP markers suggest hybridization and introgression in sympatric populations of the pleurocarpous mosses Homalothecium lutescens and H. sericeum

Fig. 2 (a) Measurement of capsule orientation in relation to the seta in Homalothecium as the angle (in degrees) between the seta and spore capsule at the basis of the spore capsule. (b) Capsule inclinations of individuals from the allopatric populations fell into the black ranges of variation; in the sympatric populations individuals occurred with capsule inclinations ranging outside typical capsule inclinations of the pure species (red zone: 150°- 164°), indicating hybrid origin

opencc-by-4.0Sep 2024View details →

Figure 4 in Introgression of bacterial leaf blight (BLB) resistant gene, Xa7 into MARDI elite variety, MR219 by marker assisted backcrossing (MABC) approach

Figure 4. PCR-based genetic polymorphism analysis of Xa7 gene closed linked, ID7 marker. Agarose gel profile of backcrossed progenies in 2% (w/v) of 1X TBE agarose gel. Lane L: 100bp DNA ladder. Lanes D and R represent IRBB7 and MR219 respectively. Line 1-22: (1) PB-2-91, (2) PB-2-107, (3) PB-2-156, (4) PB-2-224, (5) PB-2-234, (6) PB-2-238, (7) PB-2-258, (8) PB-2-29, (9) PB-2-77, (10) PB-2-226, (11) PC3-26-2, (12) PC-39-3, (13) PB-2-34, (14) PB-2-35, (15) PB-2-150, (16) PB-2-223, (17) PB-2-252, (18) PC-3-14-3, (19) PC-3-23-1, (20) PB-2-32, (21) PC3-5-2, (22) MR263.

opencc-by-4.0Sep 2024View details →

Figure 3 in Introgression of bacterial leaf blight (BLB) resistant gene, Xa7 into MARDI elite variety, MR219 by marker assisted backcrossing (MABC) approach

Figure 3. Differential response of parents. (A) MR263, (B) CL2, (C) IRBB7 and (D) MR219, respectively after being inoculated with Xanthomonas oryzae pv. oryzae at 14 DAI.