Sponge diversification in marine lakes: implications for phylogeography and population genomic studies on sponges
Data files
Mar 10, 2023 version files 3.69 GB
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Bacterial_Loci.fasta
1.76 KB
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exact.fasta
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exact.fasta.fai
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README.md
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Reference.fasta
850.92 KB
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Reference.fasta.fai
301.25 KB
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RGLB023A_AAGGA_sorted.bam
9.83 MB
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RGLB023A_AATTA_sorted.bam
12.39 MB
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RGLB023A_ACACA_sorted.bam
11.56 MB
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RGLB023A_ACGGT_sorted.bam
6.51 MB
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RGLB023A_ACTGG_sorted.bam
11.73 MB
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RGLB023A_ACTTC_sorted.bam
17.67 MB
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RGLB023A_AGCTA_sorted.bam
9.59 MB
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RGLB023A_ATACG_sorted.bam
10.96 MB
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RGLB023A_ATGAG_sorted.bam
10.23 MB
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RGLB023A_CAACC_sorted.bam
12.33 MB
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RGLB023A_CGATC_sorted.bam
8.10 MB
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RGLB023A_CTGCG_sorted.bam
13.39 MB
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RGLB023A_CTGTC_sorted.bam
8.64 MB
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RGLB023A_CTTGG_sorted.bam
19.26 MB
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RGLB023A_GACAC_sorted.bam
10.89 MB
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RGLB023A_GAGAT_sorted.bam
11.57 MB
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RGLB023A_GGTTG_sorted.bam
6.04 MB
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RGLB023A_TCGAT_sorted.bam
7.71 MB
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RGLB023A_TGCAT_sorted.bam
4.64 MB
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RGLB023B_AACCA_sorted.bam
1.67 MB
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RGLB023B_AAGGA_sorted.bam
10.82 MB
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RGLB023B_AATTA_sorted.bam
28.19 MB
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RGLB023B_ACACA_sorted.bam
2.87 MB
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RGLB023B_ACGGT_sorted.bam
1.68 MB
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RGLB023B_ACTGG_sorted.bam
7.43 MB
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RGLB023B_AGCTA_sorted.bam
13.21 MB
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RGLB023B_ATACG_sorted.bam
2.96 MB
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RGLB023B_CAACC_sorted.bam
15.59 MB
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RGLB023B_CGATC_sorted.bam
4.31 MB
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RGLB023B_GAGAT_sorted.bam
12.66 MB
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RGLB023B_GCATG_sorted.bam
30.87 MB
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RGLB023B_TCGAT_sorted.bam
12.35 MB
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RGLB023B_TGCAT_sorted.bam
11.65 MB
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RGLB023C_AAGGA_sorted.bam
72.01 MB
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RGLB023C_AATTA_sorted.bam
87 MB
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RGLB023C_ACACA_sorted.bam
113.97 MB
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RGLB023C_ACTGG_sorted.bam
162.90 MB
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RGLB023C_ACTTC_sorted.bam
118.11 MB
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RGLB023C_AGCTA_sorted.bam
89.70 MB
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RGLB023C_ATACG_sorted.bam
132.68 MB
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RGLB023C_ATGAG_sorted.bam
334.80 KB
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RGLB023C_CGATC_sorted.bam
4.95 MB
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RGLB023C_CTGCG_sorted.bam
1.20 MB
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RGLB023C_CTGTC_sorted.bam
262.99 KB
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RGLB023C_CTTGG_sorted.bam
1.77 MB
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RGLB023C_GACAC_sorted.bam
1.45 MB
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RGLB023C_GAGAT_sorted.bam
3.24 MB
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RGLB023C_GGTTG_sorted.bam
8.26 MB
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RGLB023C_TCGAT_sorted.bam
7.83 MB
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RGLB023C_TGCAT_sorted.bam
5.23 MB
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RGLB023D_ACGGT_sorted.bam
817.26 KB
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RGLB023D_ACTGG_sorted.bam
1.16 MB
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RGLB023D_ACTTC_sorted.bam
955.14 KB
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RGLB023D_AGCTA_sorted.bam
543.44 KB
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RGLB023D_ATGAG_sorted.bam
696.05 KB
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RGLB023D_CAACC_sorted.bam
734.53 KB
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RGLB023D_CGATC_sorted.bam
911.69 KB
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RGLB023D_CTGCG_sorted.bam
1.23 MB
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RGLB023D_CTGTC_sorted.bam
788.31 KB
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RGLB023D_GACAC_sorted.bam
1.03 MB
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RGLB023D_GAGAT_sorted.bam
452.23 KB
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RGLB023D_GCATG_sorted.bam
2.10 MB
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RGLB023D_TCGAT_sorted.bam
1.34 MB
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RGLB023D_TGCAT_sorted.bam
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RGLB023E_AATTA_sorted.bam
141.15 MB
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RGLB023E_ACACA_sorted.bam
90.86 MB
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RGLB023E_ACGGT_sorted.bam
89.05 MB
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RGLB023E_ACTGG_sorted.bam
76.76 MB
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RGLB023E_ACTTC_sorted.bam
182.46 MB
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RGLB023E_ATACG_sorted.bam
83.08 MB
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RGLB023E_CAACC_sorted.bam
18.90 MB
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RGLB023E_CTGCG_sorted.bam
103.75 MB
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RGLB023E_CTGTC_sorted.bam
55.53 MB
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RGLB023E_GACAC_sorted.bam
84.04 MB
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RGLB023E_GAGAT_sorted.bam
105.62 MB
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RGLB023E_GGTTG_sorted.bam
14.92 MB
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RGLB023F_AACCA_sorted.bam
92.35 MB
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RGLB023F_AATTA_sorted.bam
268 MB
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RGLB023F_ACGGT_sorted.bam
132.22 MB
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RGLB023F_ACTGG_sorted.bam
5.03 MB
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RGLB023F_ACTTC_sorted.bam
7.48 MB
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RGLB023F_ATACG_sorted.bam
20.55 MB
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RGLB023F_ATGAG_sorted.bam
6.14 MB
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RGLB023F_CAACC_sorted.bam
136.07 MB
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RGLB023F_CTGCG_sorted.bam
7.06 MB
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RGLB023F_CTGTC_sorted.bam
7.69 MB
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RGLB023F_CTTGG_sorted.bam
7.59 MB
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RGLB023F_GACAC_sorted.bam
5.85 MB
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RGLB023F_GAGAT_sorted.bam
11.94 MB
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RGLB023F_GGTTG_sorted.bam
209.22 MB
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RGLB023F_TCGAT_sorted.bam
97.78 MB
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RGLB023F_TGCAT_sorted.bam
61.50 MB
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RGLB023G_AACCA_sorted.bam
11.05 MB
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RGLB023G_AAGGA_sorted.bam
6.11 MB
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RGLB023G_AATTA_sorted.bam
7.66 MB
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RGLB023G_ACACA_sorted.bam
5.41 MB
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RGLB023G_ACGGT_sorted.bam
5.75 MB
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RGLB023G_ACTGG_sorted.bam
9.28 MB
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RGLB023G_ACTTC_sorted.bam
22.82 MB
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RGLB023G_AGCTA_sorted.bam
5.44 MB
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RGLB023G_ATACG_sorted.bam
15.27 MB
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RGLB023G_ATGAG_sorted.bam
16.20 MB
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RGLB023G_CAACC_sorted.bam
7.99 MB
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RGLB023G_CTGCG_sorted.bam
12.44 MB
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RGLB023G_CTTGG_sorted.bam
30.43 MB
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RGLB023G_GACAC_sorted.bam
13.69 MB
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RGLB023G_GAGAT_sorted.bam
11.66 MB
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RGLB023G_GCATG_sorted.bam
9.55 MB
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RGLB023G_TCGAT_sorted.bam
9.55 MB
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RGLB023G_TGCAT_sorted.bam
2.61 MB
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RGLB023H_AACCA_sorted.bam
13.79 MB
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RGLB023H_AAGGA_sorted.bam
14.04 MB
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RGLB023H_AATTA_sorted.bam
4.91 MB
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RGLB023H_ACTGG_sorted.bam
11.85 MB
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RGLB023H_ACTTC_sorted.bam
12.44 MB
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RGLB023H_AGCTA_sorted.bam
10.89 MB
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RGLB023H_ATACG_sorted.bam
17.08 MB
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RGLB023H_ATGAG_sorted.bam
7.59 MB
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RGLB023H_CAACC_sorted.bam
9.81 MB
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RGLB023H_CGATC_sorted.bam
6.61 MB
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RGLB023H_CTGCG_sorted.bam
16.31 MB
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RGLB023H_CTGTC_sorted.bam
17.32 MB
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RGLB023H_GCATG_sorted.bam
16.44 MB
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RGLB023H_GGTTG_sorted.bam
9.12 MB
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RGLB023H_TGCAT_sorted.bam
5.93 MB
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SampleList_Suberites.txt
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Sites_passed_filters.keep
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Sites_passed_filters.keep.bin
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Sites_passed_filters.keep.idx
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Sites_passed_filters.rf
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Abstract
The relative influence of geography, currents and environment on gene flow within sessile marine species remains an open question. Detecting subtle genetic differentiation at small scales is challenging in benthic populations due to large effective population sizes, general lack of resolution in genetic markers, and because barriers to dispersal often remain elusive. Marine lakes can circumvent confounding factors by providing discrete and replicated ecosystems. Using high-resolution double digest restriction-site associated DNA sequencing (4,826 Single Nucleotide Polymorphisms, SNPs), we genotyped populations of the sponge Suberites diversicolor (n=125) to test the relative importance of spatial scales (1-1,400km), local environmental regimes, and permeability of seascape barriers in shaping population genomic structure. With the SNP dataset we show strong intra-lineage population structure, even at scales <10km (average FST = 0.63), that was not detected previously using single markers. Most variation was explained by differentiation between populations (AMOVA: 48.8%) with signatures of population size declines and bottlenecks per lake. Though the populations were strongly structured, we did not detect significant effects of geographic distance, local environments, or degree of connection to the sea on population structure, suggesting mechanisms such as founder events with subsequent priority effects may be at play. We show that the inclusion of morphologically cryptic lineages that can be detected with the COI marker can reduce the obtained SNP set by almost 90%. Future work on sponge genomics should confirm that only one lineage is included. Our results call for a reassessment of poorly dispersing benthic organisms that were previously assumed to be highly connected based on low-resolution markers.
Tissue samples from the sponge Suberites diversicolor were sampled from two lagoon locations and nine marine lakes in the Indo-Pacific (Australia and Indonesia). DNA was extracted using the Blood & Tissue kit from Qiagen. In total 125 individuals were successfully sequenced using Illumina HiSeq 2500, employing a RAD-seq strategy. Custom scripts (provided) and open source programs (see methodology of paper) were employed to create a de-novo reference and align reads.