An examination of seasonal variation in taxonomic richness and community composition using eDNA on a tropical coral reef
Data files
Nov 21, 2024 version files 15.31 GB
-
LI_sampling_metadata__Final__July_7__2023.csv
18.75 KB
-
LIRS_12_01_20_1_16S_Fish.fastq
54.41 MB
-
LIRS_12_01_20_1_CP1_R1.fastq
50.87 MB
-
LIRS_12_01_20_1_CP1_R2.fastq
49.90 MB
-
LIRS_12_01_20_1_CP2_R1.fastq
55.13 MB
-
LIRS_12_01_20_1_CP2_R2.fastq
55.13 MB
-
LIRS_12_01_20_2_16S_Fish.fastq
35.06 MB
-
LIRS_12_01_20_2_CP1_R1.fastq
62.34 MB
-
LIRS_12_01_20_2_CP1_R2.fastq
61.14 MB
-
LIRS_12_01_20_2_CP2_R1.fastq
38.52 MB
-
LIRS_12_01_20_2_CP2_R2.fastq
38.52 MB
-
LIRS_12_01_20_3_16S_Fish.fastq
52.58 MB
-
LIRS_12_01_20_3_CP1_R1.fastq
77.43 MB
-
LIRS_12_01_20_3_CP1_R2.fastq
75.94 MB
-
LIRS_12_01_20_3_CP2_R1.fastq
31.54 MB
-
LIRS_12_01_20_3_CP2_R2.fastq
31.54 MB
-
LIRS_12_01_20_4_16S_Fish.fastq
52.99 MB
-
LIRS_12_01_20_4_CP1_R1.fastq
51.41 MB
-
LIRS_12_01_20_4_CP1_R2.fastq
50.42 MB
-
LIRS_12_01_20_4_CP2_R1.fastq
42.96 MB
-
LIRS_12_01_20_4_CP2_R2.fastq
42.96 MB
-
LIRS_12_01_20_5_16S_Fish.fastq
53.57 MB
-
LIRS_12_01_20_5_CP1_R1.fastq
37.33 MB
-
LIRS_12_01_20_5_CP1_R2.fastq
36.61 MB
-
LIRS_12_01_20_5_CP2_R1.fastq
30.23 MB
-
LIRS_12_01_20_5_CP2_R2.fastq
30.23 MB
-
LIRS_12_01_20_6_16S_Fish.fastq
491 B
-
LIRS_12_01_20_6_CP1_R1.fastq
48.41 MB
-
LIRS_12_01_20_6_CP1_R2.fastq
47.48 MB
-
LIRS_12_01_20_6_CP2_R1.fastq
66.09 MB
-
LIRS_12_01_20_6_CP2_R2.fastq
66.09 MB
-
LIRS_12_02_19_1_16S_Fish.fastq
70 MB
-
LIRS_12_02_19_1_CP1_R1.fastq
54.25 MB
-
LIRS_12_02_19_1_CP1_R2.fastq
53.20 MB
-
LIRS_12_02_19_1_CP2_R1.fastq
35.13 MB
-
LIRS_12_02_19_1_CP2_R2.fastq
35.13 MB
-
LIRS_12_02_19_2_16S_Fish.fastq
49.96 MB
-
LIRS_12_02_19_2_CP1_R1.fastq
56.53 MB
-
LIRS_12_02_19_2_CP1_R2.fastq
55.44 MB
-
LIRS_12_02_19_2_CP2_R1.fastq
50.74 MB
-
LIRS_12_02_19_2_CP2_R2.fastq
50.74 MB
-
LIRS_12_02_19_3_16S_Fish.fastq
50.85 MB
-
LIRS_12_02_19_3_CP1_R1.fastq
43.86 MB
-
LIRS_12_02_19_3_CP1_R2.fastq
43.01 MB
-
LIRS_12_02_19_3_CP2_R1.fastq
35.26 MB
-
LIRS_12_02_19_3_CP2_R2.fastq
35.26 MB
-
LIRS_12_02_19_4_16S_Fish.fastq
104.46 MB
-
LIRS_12_02_19_4_CP1_R1.fastq
66.06 MB
-
LIRS_12_02_19_4_CP1_R2.fastq
64.79 MB
-
LIRS_12_02_19_4_CP2_R1.fastq
56.34 MB
-
LIRS_12_02_19_4_CP2_R2.fastq
56.34 MB
-
LIRS_12_02_19_5_16S_Fish.fastq
107.03 MB
-
LIRS_12_02_19_5_CP1_R1.fastq
45.25 MB
-
LIRS_12_02_19_5_CP1_R2.fastq
44.38 MB
-
LIRS_12_02_19_5_CP2_R1.fastq
53.98 MB
-
LIRS_12_02_19_5_CP2_R2.fastq
53.98 MB
-
LIRS_12_02_19_6_16S_Fish.fastq
27.90 KB
-
LIRS_12_02_19_6_CP1_R1.fastq
19.74 KB
-
LIRS_12_02_19_6_CP1_R2.fastq
19.36 KB
-
LIRS_12_02_19_6_CP2_R1.fastq
31.81 KB
-
LIRS_12_02_19_6_CP2_R2.fastq
31.81 KB
-
LIRS_12_03_19_1_16S_Fish.fastq
88.39 MB
-
LIRS_12_03_19_1_CP1_R1.fastq
51.42 MB
-
LIRS_12_03_19_1_CP1_R2.fastq
50.43 MB
-
LIRS_12_03_19_1_CP2_R1.fastq
46.76 MB
-
LIRS_12_03_19_1_CP2_R2.fastq
46.94 MB
-
LIRS_12_03_19_2_16S_Fish.fastq
101.83 MB
-
LIRS_12_03_19_2_CP1_R1.fastq
24.64 MB
-
LIRS_12_03_19_2_CP1_R2.fastq
24.17 MB
-
LIRS_12_03_19_2_CP2_R1.fastq
38.08 MB
-
LIRS_12_03_19_2_CP2_R2.fastq
38.22 MB
-
LIRS_12_03_19_3_16S_Fish.fastq
39.69 MB
-
LIRS_12_03_19_3_CP1_R1.fastq
46.90 MB
-
LIRS_12_03_19_3_CP1_R2.fastq
46 MB
-
LIRS_12_03_19_3_CP2_R1.fastq
62.12 MB
-
LIRS_12_03_19_3_CP2_R2.fastq
62.36 MB
-
LIRS_12_03_19_4_16S_Fish.fastq
51.33 MB
-
LIRS_12_03_19_4_CP1_R1.fastq
41.89 MB
-
LIRS_12_03_19_4_CP1_R2.fastq
41.08 MB
-
LIRS_12_03_19_4_CP2_R1.fastq
71.75 MB
-
LIRS_12_03_19_4_CP2_R2.fastq
72.02 MB
-
LIRS_12_03_19_5_16S_Fish.fastq
95.84 MB
-
LIRS_12_03_19_5_CP1_R1.fastq
35.33 MB
-
LIRS_12_03_19_5_CP1_R2.fastq
34.65 MB
-
LIRS_12_03_19_5_CP2_R1.fastq
53.74 MB
-
LIRS_12_03_19_5_CP2_R2.fastq
53.94 MB
-
LIRS_12_03_19_6_16S_Fish.fastq
42.10 MB
-
LIRS_12_03_19_6_CP1_R1.fastq
28.60 MB
-
LIRS_12_03_19_6_CP1_R2.fastq
28.05 MB
-
LIRS_12_03_19_6_CP2_R1.fastq
40.25 MB
-
LIRS_12_03_19_6_CP2_R2.fastq
40.41 MB
-
LIRS_12_04_19_1_16S_Fish.fastq
44.05 MB
-
LIRS_12_04_19_1_CP1_R1.fastq
34.63 MB
-
LIRS_12_04_19_1_CP1_R2.fastq
33.96 MB
-
LIRS_12_04_19_1_CP2_R1.fastq
37.44 MB
-
LIRS_12_04_19_1_CP2_R2.fastq
37.58 MB
-
LIRS_12_04_19_2_16S_Fish.fastq
55.35 MB
-
LIRS_12_04_19_2_CP1_R1.fastq
473.29 KB
-
LIRS_12_04_19_2_CP1_R2.fastq
464.18 KB
-
LIRS_12_04_19_2_CP2_R1.fastq
23.47 MB
-
LIRS_12_04_19_2_CP2_R2.fastq
23.56 MB
-
LIRS_12_04_19_3_16S_Fish.fastq
62.97 MB
-
LIRS_12_04_19_3_CP1_R1.fastq
58 MB
-
LIRS_12_04_19_3_CP1_R2.fastq
56.88 MB
-
LIRS_12_04_19_3_CP2_R1.fastq
59.72 MB
-
LIRS_12_04_19_3_CP2_R2.fastq
59.95 MB
-
LIRS_12_04_19_4_16S_Fish.fastq
39.58 MB
-
LIRS_12_04_19_4_CP1_R1.fastq
46.10 MB
-
LIRS_12_04_19_4_CP1_R2.fastq
45.21 MB
-
LIRS_12_04_19_4_CP2_R1.fastq
47.18 MB
-
LIRS_12_04_19_4_CP2_R2.fastq
47.36 MB
-
LIRS_12_04_19_5_16S_Fish.fastq
987 B
-
LIRS_12_04_19_5_CP1_R1.fastq
47.17 MB
-
LIRS_12_04_19_5_CP1_R2.fastq
46.27 MB
-
LIRS_12_04_19_5_CP2_R1.fastq
36.77 MB
-
LIRS_12_04_19_5_CP2_R2.fastq
36.91 MB
-
LIRS_12_04_19_6_16S_Fish.fastq
88.48 MB
-
LIRS_12_04_19_6_CP1_R1.fastq
53.06 MB
-
LIRS_12_04_19_6_CP1_R2.fastq
52.04 MB
-
LIRS_12_04_19_6_CP2_R1.fastq
38.21 MB
-
LIRS_12_04_19_6_CP2_R2.fastq
38.36 MB
-
LIRS_12_06_19_1_16S_Fish.fastq
29.24 MB
-
LIRS_12_06_19_1_CP1_R1.fastq
8.31 KB
-
LIRS_12_06_19_1_CP1_R2.fastq
8.15 KB
-
LIRS_12_06_19_1_CP2_R1.fastq
82.47 MB
-
LIRS_12_06_19_1_CP2_R2.fastq
82.78 MB
-
LIRS_12_06_19_2_16S_Fish.fastq
988 B
-
LIRS_12_06_19_2_CP1_R1.fastq
60.36 MB
-
LIRS_12_06_19_2_CP1_R2.fastq
59.20 MB
-
LIRS_12_06_19_2_CP2_R1.fastq
76.22 MB
-
LIRS_12_06_19_2_CP2_R2.fastq
76.52 MB
-
LIRS_12_06_19_3_16S_Fish.fastq
24.64 MB
-
LIRS_12_06_19_3_CP1_R1.fastq
29.09 KB
-
LIRS_12_06_19_3_CP1_R2.fastq
28.53 KB
-
LIRS_12_06_19_3_CP2_R1.fastq
88.45 MB
-
LIRS_12_06_19_3_CP2_R2.fastq
88.79 MB
-
LIRS_12_06_19_4_16S_Fish.fastq
987 B
-
LIRS_12_06_19_4_CP2_R1.fastq
14.03 KB
-
LIRS_12_06_19_4_CP2_R2.fastq
14.08 KB
-
LIRS_12_06_19_5_16S_Fish.fastq
25.23 MB
-
LIRS_12_06_19_5_CP1_R1.fastq
36.49 MB
-
LIRS_12_06_19_5_CP1_R2.fastq
35.79 MB
-
LIRS_12_06_19_5_CP2_R1.fastq
52.67 MB
-
LIRS_12_06_19_5_CP2_R2.fastq
52.88 MB
-
LIRS_12_06_19_6_16S_Fish.fastq
10.81 KB
-
LIRS_12_06_19_6_CP1_R1.fastq
520 B
-
LIRS_12_06_19_6_CP1_R2.fastq
510 B
-
LIRS_12_06_19_6_CP2_R1.fastq
31.69 KB
-
LIRS_12_06_19_6_CP2_R2.fastq
31.81 KB
-
LIRS_12_07_19_1_16S_Fish.fastq
2.30 MB
-
LIRS_12_07_19_1_CP1_R1.fastq
144.96 KB
-
LIRS_12_07_19_1_CP1_R2.fastq
142.17 KB
-
LIRS_12_07_19_1_CP2_R1.fastq
65.55 MB
-
LIRS_12_07_19_1_CP2_R2.fastq
65.80 MB
-
LIRS_12_07_19_2_16S_Fish.fastq
8.93 MB
-
LIRS_12_07_19_2_CP1_R1.fastq
8.83 KB
-
LIRS_12_07_19_2_CP1_R2.fastq
8.66 KB
-
LIRS_12_07_19_2_CP2_R1.fastq
23.43 MB
-
LIRS_12_07_19_2_CP2_R2.fastq
23.52 MB
-
LIRS_12_07_19_3_16S_Fish.fastq
23.38 MB
-
LIRS_12_07_19_3_CP1_R1.fastq
4.16 KB
-
LIRS_12_07_19_3_CP1_R2.fastq
4.08 KB
-
LIRS_12_07_19_3_CP2_R1.fastq
1.90 MB
-
LIRS_12_07_19_3_CP2_R2.fastq
1.91 MB
-
LIRS_12_07_19_4_16S_Fish.fastq
990 B
-
LIRS_12_07_19_4_CP1_R1.fastq
8.84 KB
-
LIRS_12_07_19_4_CP1_R2.fastq
8.66 KB
-
LIRS_12_07_19_4_CP2_R1.fastq
30.79 MB
-
LIRS_12_07_19_4_CP2_R2.fastq
30.91 MB
-
LIRS_12_07_19_5_16S_Fish.fastq
27.36 KB
-
LIRS_12_07_19_5_CP2_R1.fastq
9.92 MB
-
LIRS_12_07_19_5_CP2_R2.fastq
9.96 MB
-
LIRS_12_07_19_6_16S_Fish.fastq
15.42 MB
-
LIRS_12_07_19_6_CP1_R1.fastq
81.49 MB
-
LIRS_12_07_19_6_CP1_R2.fastq
79.92 MB
-
LIRS_12_07_19_6_CP2_R1.fastq
42.45 MB
-
LIRS_12_07_19_6_CP2_R2.fastq
42.61 MB
-
LIRS_12_09_19_1_16S_Fish.fastq
53.94 MB
-
LIRS_12_09_19_1_CP1_R1.fastq
24.27 MB
-
LIRS_12_09_19_1_CP1_R2.fastq
23.80 MB
-
LIRS_12_09_19_1_CP2_R1.fastq
87.47 MB
-
LIRS_12_09_19_1_CP2_R2.fastq
87.47 MB
-
LIRS_12_09_19_2_16S_Fish.fastq
59.93 MB
-
LIRS_12_09_19_2_CP1_R1.fastq
43.04 MB
-
LIRS_12_09_19_2_CP1_R2.fastq
42.21 MB
-
LIRS_12_09_19_2_CP2_R1.fastq
41.48 MB
-
LIRS_12_09_19_2_CP2_R2.fastq
41.48 MB
-
LIRS_12_09_19_3_16S_Fish.fastq
53.39 MB
-
LIRS_12_09_19_3_CP1_R1.fastq
67.03 MB
-
LIRS_12_09_19_3_CP1_R2.fastq
65.74 MB
-
LIRS_12_09_19_3_CP2_R1.fastq
58.23 MB
-
LIRS_12_09_19_3_CP2_R2.fastq
58.23 MB
-
LIRS_12_09_19_4_16S_Fish.fastq
66.09 MB
-
LIRS_12_09_19_4_CP1_R1.fastq
56.67 MB
-
LIRS_12_09_19_4_CP1_R2.fastq
55.58 MB
-
LIRS_12_09_19_4_CP2_R1.fastq
49.03 MB
-
LIRS_12_09_19_4_CP2_R2.fastq
49.03 MB
-
LIRS_12_09_19_5_16S_Fish.fastq
53.69 MB
-
LIRS_12_09_19_5_CP1_R1.fastq
45.68 MB
-
LIRS_12_09_19_5_CP1_R2.fastq
44.80 MB
-
LIRS_12_09_19_5_CP2_R1.fastq
46.58 MB
-
LIRS_12_09_19_5_CP2_R2.fastq
46.58 MB
-
LIRS_12_09_19_6_16S_Fish.fastq
38.35 MB
-
LIRS_12_09_19_6_CP1_R1.fastq
80.05 MB
-
LIRS_12_09_19_6_CP1_R2.fastq
78.50 MB
-
LIRS_12_09_19_6_CP2_R1.fastq
43.71 MB
-
LIRS_12_09_19_6_CP2_R2.fastq
43.71 MB
-
LIRS_12_10_19_1_16S_Fish.fastq
37.23 MB
-
LIRS_12_10_19_1_CP1_R1.fastq
41.98 MB
-
LIRS_12_10_19_1_CP1_R2.fastq
41.17 MB
-
LIRS_12_10_19_1_CP2_R1.fastq
52.64 MB
-
LIRS_12_10_19_1_CP2_R2.fastq
52.64 MB
-
LIRS_12_10_19_2_16S_Fish.fastq
45.14 MB
-
LIRS_12_10_19_2_CP1_R1.fastq
40.19 MB
-
LIRS_12_10_19_2_CP1_R2.fastq
39.42 MB
-
LIRS_12_10_19_2_CP2_R1.fastq
46.72 MB
-
LIRS_12_10_19_2_CP2_R2.fastq
46.72 MB
-
LIRS_12_10_19_3_16S_Fish.fastq
65.59 MB
-
LIRS_12_10_19_3_CP1_R1.fastq
45.34 MB
-
LIRS_12_10_19_3_CP1_R2.fastq
44.47 MB
-
LIRS_12_10_19_3_CP2_R1.fastq
58.12 MB
-
LIRS_12_10_19_3_CP2_R2.fastq
58.12 MB
-
LIRS_12_10_19_4_16S_Fish.fastq
3.98 KB
-
LIRS_12_10_19_4_CP1_R1.fastq
29.34 MB
-
LIRS_12_10_19_4_CP1_R2.fastq
28.77 MB
-
LIRS_12_10_19_4_CP2_R1.fastq
31.01 MB
-
LIRS_12_10_19_4_CP2_R2.fastq
31.01 MB
-
LIRS_12_10_19_5_16S_Fish.fastq
66.57 MB
-
LIRS_12_10_19_5_CP1_R1.fastq
43.53 MB
-
LIRS_12_10_19_5_CP1_R2.fastq
42.70 MB
-
LIRS_12_10_19_5_CP2_R1.fastq
52.87 MB
-
LIRS_12_10_19_5_CP2_R2.fastq
52.87 MB
-
LIRS_12_10_19_6_16S_Fish.fastq
49.90 MB
-
LIRS_12_10_19_6_CP1_R1.fastq
36.39 MB
-
LIRS_12_10_19_6_CP1_R2.fastq
35.69 MB
-
LIRS_12_10_19_6_CP2_R1.fastq
61.29 MB
-
LIRS_12_10_19_6_CP2_R2.fastq
61.29 MB
-
LIRS_13_05_19_1_16S_Fish.fastq
63.34 MB
-
LIRS_13_05_19_1_CP1_R1.fastq
52.82 MB
-
LIRS_13_05_19_1_CP1_R2.fastq
51.80 MB
-
LIRS_13_05_19_1_CP2_R1.fastq
86.77 MB
-
LIRS_13_05_19_1_CP2_R2.fastq
87.10 MB
-
LIRS_13_05_19_2_16S_Fish.fastq
36.82 MB
-
LIRS_13_05_19_2_CP1_R1.fastq
41.71 MB
-
LIRS_13_05_19_2_CP1_R2.fastq
40.90 MB
-
LIRS_13_05_19_2_CP2_R1.fastq
333.01 KB
-
LIRS_13_05_19_2_CP2_R2.fastq
334.29 KB
-
LIRS_13_05_19_3_16S_Fish.fastq
43.99 MB
-
LIRS_13_05_19_3_CP1_R1.fastq
53.43 MB
-
LIRS_13_05_19_3_CP1_R2.fastq
52.40 MB
-
LIRS_13_05_19_3_CP2_R1.fastq
49.33 MB
-
LIRS_13_05_19_3_CP2_R2.fastq
49.52 MB
-
LIRS_13_05_19_4_16S_Fish.fastq
25.45 MB
-
LIRS_13_05_19_4_CP1_R1.fastq
6.54 MB
-
LIRS_13_05_19_4_CP1_R2.fastq
6.42 MB
-
LIRS_13_05_19_4_CP2_R1.fastq
79.94 MB
-
LIRS_13_05_19_4_CP2_R2.fastq
80.24 MB
-
LIRS_13_05_19_5_16S_Fish.fastq
29.27 MB
-
LIRS_13_05_19_5_CP1_R1.fastq
47.64 MB
-
LIRS_13_05_19_5_CP1_R2.fastq
46.73 MB
-
LIRS_13_05_19_5_CP2_R1.fastq
79.75 MB
-
LIRS_13_05_19_5_CP2_R2.fastq
80.05 MB
-
LIRS_13_05_19_6_16S_Fish.fastq
15.44 MB
-
LIRS_13_05_19_6_CP2_R1.fastq
72.15 MB
-
LIRS_13_05_19_6_CP2_R2.fastq
72.42 MB
-
LIRS_13_08_19_1_16S_Fish.fastq
31.30 MB
-
LIRS_13_08_19_1_CP1_R1.fastq
19.44 MB
-
LIRS_13_08_19_1_CP1_R2.fastq
19.07 MB
-
LIRS_13_08_19_1_CP2_R1.fastq
46.47 MB
-
LIRS_13_08_19_1_CP2_R2.fastq
46.64 MB
-
LIRS_13_08_19_2_16S_Fish.fastq
37.88 MB
-
LIRS_13_08_19_2_CP1_R1.fastq
90.88 MB
-
LIRS_13_08_19_2_CP1_R2.fastq
89.13 MB
-
LIRS_13_08_19_2_CP2_R1.fastq
34.19 MB
-
LIRS_13_08_19_2_CP2_R2.fastq
34.32 MB
-
LIRS_13_08_19_3_16S_Fish.fastq
36.77 MB
-
LIRS_13_08_19_3_CP1_R1.fastq
20.76 MB
-
LIRS_13_08_19_3_CP1_R2.fastq
20.36 MB
-
LIRS_13_08_19_3_CP2_R1.fastq
112.32 MB
-
LIRS_13_08_19_3_CP2_R2.fastq
112.75 MB
-
LIRS_13_08_19_4_16S_Fish.fastq
49.84 MB
-
LIRS_13_08_19_4_CP1_R1.fastq
28.57 KB
-
LIRS_13_08_19_4_CP1_R2.fastq
28.02 KB
-
LIRS_13_08_19_4_CP2_R1.fastq
6.74 MB
-
LIRS_13_08_19_4_CP2_R2.fastq
6.76 MB
-
LIRS_13_08_19_5_16S_Fish.fastq
84.92 MB
-
LIRS_13_08_19_5_CP1_R1.fastq
27.16 MB
-
LIRS_13_08_19_5_CP1_R2.fastq
26.64 MB
-
LIRS_13_08_19_5_CP2_R1.fastq
51.13 MB
-
LIRS_13_08_19_5_CP2_R2.fastq
51.33 MB
-
LIRS_13_08_19_6_16S_Fish.fastq
23.37 MB
-
LIRS_13_08_19_6_CP1_R1.fastq
17.14 KB
-
LIRS_13_08_19_6_CP1_R2.fastq
16.81 KB
-
LIRS_13_08_19_6_CP2_R1.fastq
38.44 KB
-
LIRS_13_08_19_6_CP2_R2.fastq
38.59 KB
-
LIRS_13_11_19_1_16S_Fish.fastq
38.61 MB
-
LIRS_13_11_19_1_CP1_R1.fastq
31.83 MB
-
LIRS_13_11_19_1_CP1_R2.fastq
31.21 MB
-
LIRS_13_11_19_1_CP2_R1.fastq
22.64 MB
-
LIRS_13_11_19_1_CP2_R2.fastq
22.64 MB
-
LIRS_13_11_19_2_16S_Fish.fastq
21.88 MB
-
LIRS_13_11_19_2_CP1_R1.fastq
35.51 MB
-
LIRS_13_11_19_2_CP1_R2.fastq
34.83 MB
-
LIRS_13_11_19_2_CP2_R1.fastq
36.03 MB
-
LIRS_13_11_19_2_CP2_R2.fastq
36.03 MB
-
LIRS_13_11_19_3_16S_Fish.fastq
57.27 MB
-
LIRS_13_11_19_3_CP1_R1.fastq
51.46 MB
-
LIRS_13_11_19_3_CP1_R2.fastq
50.47 MB
-
LIRS_13_11_19_3_CP2_R1.fastq
75.46 MB
-
LIRS_13_11_19_3_CP2_R2.fastq
75.46 MB
-
LIRS_13_11_19_4_16S_Fish.fastq
94.84 MB
-
LIRS_13_11_19_4_CP1_R1.fastq
40.47 MB
-
LIRS_13_11_19_4_CP1_R2.fastq
39.69 MB
-
LIRS_13_11_19_4_CP2_R1.fastq
55.62 MB
-
LIRS_13_11_19_4_CP2_R2.fastq
55.62 MB
-
LIRS_13_11_19_5_16S_Fish.fastq
63.85 MB
-
LIRS_13_11_19_5_CP1_R1.fastq
44.91 MB
-
LIRS_13_11_19_5_CP1_R2.fastq
44.05 MB
-
LIRS_13_11_19_5_CP2_R1.fastq
114.98 MB
-
LIRS_13_11_19_5_CP2_R2.fastq
114.98 MB
-
LIRS_13_11_19_6_16S_Fish.fastq
71.73 MB
-
LIRS_13_11_19_6_CP1_R1.fastq
68.45 MB
-
LIRS_13_11_19_6_CP1_R2.fastq
67.13 MB
-
LIRS_13_11_19_6_CP2_R1.fastq
41.85 MB
-
LIRS_13_11_19_6_CP2_R2.fastq
41.85 MB
-
LIRS_13_12_19_1_16S_Fish.fastq
63.02 MB
-
LIRS_13_12_19_1_CP1_R1.fastq
42.58 MB
-
LIRS_13_12_19_1_CP1_R2.fastq
41.76 MB
-
LIRS_13_12_19_1_CP2_R1.fastq
41.71 MB
-
LIRS_13_12_19_1_CP2_R2.fastq
41.71 MB
-
LIRS_13_12_19_2_16S_Fish.fastq
38.18 MB
-
LIRS_13_12_19_2_CP1_R1.fastq
45.74 MB
-
LIRS_13_12_19_2_CP1_R2.fastq
44.86 MB
-
LIRS_13_12_19_2_CP2_R1.fastq
37.09 MB
-
LIRS_13_12_19_2_CP2_R2.fastq
37.09 MB
-
LIRS_13_12_19_3_16S_Fish.fastq
37.58 MB
-
LIRS_13_12_19_3_CP1_R1.fastq
44.23 MB
-
LIRS_13_12_19_3_CP1_R2.fastq
43.38 MB
-
LIRS_13_12_19_3_CP2_R1.fastq
47.91 MB
-
LIRS_13_12_19_3_CP2_R2.fastq
47.91 MB
-
LIRS_13_12_19_4_16S_Fish.fastq
33.18 MB
-
LIRS_13_12_19_4_CP1_R1.fastq
44.30 MB
-
LIRS_13_12_19_4_CP1_R2.fastq
43.45 MB
-
LIRS_13_12_19_4_CP2_R1.fastq
48.71 MB
-
LIRS_13_12_19_4_CP2_R2.fastq
48.71 MB
-
LIRS_13_12_19_5_16S_Fish.fastq
36.24 MB
-
LIRS_13_12_19_5_CP1_R1.fastq
43.87 MB
-
LIRS_13_12_19_5_CP1_R2.fastq
43.02 MB
-
LIRS_13_12_19_5_CP2_R1.fastq
39.46 MB
-
LIRS_13_12_19_5_CP2_R2.fastq
39.46 MB
-
LIRS_13_12_19_6_16S_Fish.fastq
57.35 MB
-
LIRS_13_12_19_6_CP1_R1.fastq
43.45 MB
-
LIRS_13_12_19_6_CP1_R2.fastq
42.61 MB
-
LIRS_13_12_19_6_CP2_R1.fastq
73.53 MB
-
LIRS_13_12_19_6_CP2_R2.fastq
73.53 MB
-
README.md
3.74 KB
Abstract
Small volumes of water containing environmental DNA (eDNA) are increasingly combined with metabarcoding to generate biodiversity data for specific fractions of marine flora and fauna. To date, however, few studies have utilized this technique to assess how well it captures seasonal patterns in coral reef communities or how environmental or methodological factors influence eDNA detections. In our study, we used three eDNA metabarcoding assays primarily targeting bony fish, elasmobranchs, as well as cnidarians and sponges (Cnidaria/Porifera) combined with monthly seawater sampling to 1) investigate temporal variation in taxonomic detections and 2) statistically test the potential effect of season, sea surface temperature, timing of spawning (using moon phase as a proxy), and sample preservation on taxon detection across a 12-month period in a model coral reef system (Big Vicki’s Reef, Lizard Island, Great Barrier Reef, Australia). Species-level fish and genus-level scleractinian coral detections from standardised visual surveys conducted at the same coral reef, in addition to a curated list of all known fishes recorded from the more expansive coral reef system, were used to validate eDNA detections. Our eDNA dataset indicated that the number of taxa detected were consistently highest in September for fish, and in February followed by September for Cnidaria/Porifera. Conversely, detections were lowest in June and July for all taxa. Some, but not all, of the environmental and methodological variables explained the observed temporal pattern in biological communities or systematic changes in the number of taxa, and in some cases, this effect was taxon dependent. Our study also highlights the significance of timing in eDNA biodiversity surveys conducted on tropical coral reefs in the Southern Hemisphere. To obtain the most meaningful estimates of site diversity, we recommend focusing sampling efforts between early spring to early autumn. Alternatively, allocating an entire year to sampling would better capture seasonal variation and provide more comprehensive insights into coral reef biodiversity.
[Access this dataset on Dryad (doi:https://doi.org/10.5061/dryad.jq2bvq8fh)]
Description of the data and file structure
We here provide the raw demultiplexed 16S Fish (read 1 only), as well as the paired-end Coral ITS2 (CP1) and Coral ITS2_acros (CP2) assay sequence data in .fastq format. These files contain sequence data seperated into their individual sample replicates for each genetic assay. For file naming nomenclature, each file name begins with the acronym for Lizard Island Research Station (LIRS), followed by the date of sampling, followed by the replicate number, followed by the genetic assay, and in the case of paired-end sequencing runs/assays (i.e. CP1 and CP2), whether it is the read 1 set of sequences (R1) or the read 2 set of sequences (R2). For example, LIRS_12_01_20_1_16S_Fish.fastq are the DNA sequences in .fastq format obtained from the water sample collected at LIRS, on January 12, 20220, replicate 1 (of 6) samples collected on that date, and sequenced using the 16S Fish genetic assay. As another example, LIRS_12_02_19_3_CP1_R1.fastq are the DNA sequences in .fastq format obtained from the water sample collected at LIRS, on February 12, 2019, replicate 3 (of 6) samples collected on that date, run on the Coral ITS2 (CP1) genetic assay, and the R1 set of sequences. As a final example, LIRS_12_02_19_3_CP1_R2.fastq are the DNA sequences in .fastq format obtained from the water sample collected at LIRS, on February 12, 2019, replicate 3 (of 6) samples collected on that date, run on the Coral ITS2 (CP1) genetic assay, and the paired R2 et of sequences.
We also provide an excel spreadsheet listing the metadata associated with each seawater sample collected at Lizard Island, Australia named “LI_sampling_metadata__Final__July_7__2023.csv”
EMu registration number: Australian Museum voucher registration number for the archived filter paper.
Sample ID: unique sample ID based on the acronym for Lizard Island Research Station (LIRS), followed by the date of sampling, followed by the replicate (filter paper) number.
Amount filtered: amount of water pushed through each replicate filter paper in litres.
Filter size: mesh size of the filter paper used to filter water samples.
Sample processing: the person that filtered the water sample.
Sampling country: country where water sample was collected.
Sampling Location: exact location where the water sample was collected.
Reef Location: broader reef where the water sample was collected.
Exposed or Sheltered: whether water sample was collected on the exposed or sheltered side of the reef.
Latitude: latitude where the water sample was collected.
Longitude: longitude where the water sample was collected.
Sampling Date: date when the water sample was collected
Lunar Cycle: lunar position when the water sample was collected (a variable used to test associations with taxonomic richness and composition)
Days frozen: number of days the collected water sample was frozen prior to thawing and filtering. Note that 0 days frozen means the water sample was not frozen but instead filtered immediately after collection on the reef.
Sharing/Access information
These sequences and metadata were used in the following published paper:
DiBattista, J.D., West, K.M., Ceccarelli, D.M., Hoggett, A.K., Vail, L.L., Garcia, R., and Richards, Z.T. (in press) An examination of seasonal variation in taxonomic richness and community composition using eDNA on a tropical coral reef. Coral Reefs. https://doi.org/10.1007/s00338-024-02594-6
Laboratory processing
DNA was extracted from half of each filter membrane (including filtration controls) within six months of collection using the DNeasy Blood and Tissue Kit (QIAGEN) in the TrEnD Laboratory at Curtin University in Western Australia with the following modifications: 540 µl of ATL lysis buffer, 60 µl of Proteinase K, and a 3-hr digest at 56°C. An extraction blank was processed in parallel with every set of eleven samples to detect any cross-contamination. Three previously published primer sets (16S Fish, CoralITS2, and CoralITS2_acro; Table 1) were employed in this study to amplify primarily teleost fish and scleractinian coral taxa, respectively. Quantitative PCR (qPCR) was carried out in 25 μl containing the following concentrations: 1X AmpliTaq Gold® PCR buffer (Life Technologies, Massachusetts, USA), 2 mM MgCl2 (Fisher Biotec, Australia), 0.4μM dNTPs, 0.1mg BSA (Fisher Biotec, Australia), 0.4 μM each of forward and reverse primers (Integrated DNA Technologies, Australia), 0.6 μl of 5X SYBR® Green (Life Technologies), 1U AmpliTaq Gold® DNA Polymerase (Life Technologies), 2 μl of eDNA template, and made to volume with Ultrapure™ Distilled Water (Life Technologies). All qPCRs were prepared in dedicated trace DNA (clean room) facilities at the TrEnD Laboratory, Curtin University, and amplified on a StepOnePlus Real-Time PCR System (Applied Biosystems, Massachusetts, USA) with the following PCR cycling conditions: initial denaturation at 95°C for 5 min, followed by 40 cycles of 95°C for 30 s, 52-55°C for 30 s (see respective annealing temperatures in Table 1), and 72°C for 45 s, with a final extension of 72°C for 10 min. Each sample was amplified in duplicate in a single-step process via the use of fusion-tagged primer architecture, whereby original primers are flanked by a unique 6–8 bp multiplex identifier tag (MID-tag) and an Illumina compatible sequencing adapter.
MID-tagged PCR amplicons were then pooled into two libraries (the first containing 16S Fish amplicons, and the second CoralITS2 and CoralITS2_acro amplicons combined) at equimolar ratios based on qPCR ΔRn values. The two libraries were then size-selected using a Pippin-Prep (Sage Science, Beverly, USA) to remove any amplicons outside of the target range (150-450 bp, and 160-600 bp, respectively). Size-selected libraries were then purified using the QIAquick PCR Purification Kit (Qiagen, Venlo, Netherlands), quantified using a Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, USA), and diluted to 2 nM for loading onto the sequencing platform. The 16S Fish library was loaded onto a 300 cycle Illumina MiSeq® V2 Standard Flow Cell for unidirectional sequencing. The CoralITS2 library was loaded onto a 500 cycle Illumina MiSeq® V2 Standard Flow Cells for paired-end sequencing. The sequencing of both libraries was conducted on an Illumina MiSeq platform (Illumina, San Diego, USA) housed in the TrEnD Laboratory.
Bioinformatics
Sequences were demultiplexed into their respective samples based on their MID-tags using the ngsfilter and obisplit commands in OBITools (v1.2.9; Boyer et al. 2016) for the single-end (16S Fish) sequencing reads, and the insect package (Wilkinson et al. 2018) for the paired-end (CoralITS2 and CoralITS2_acro) sequencing reads. Data from the two sequencing libraries were separately quality filtered (minimum sequence length = 100 bp, maximum expected errors = 2, no ambiguous nucleotides), denoised, merged (paired-end reads only, 20 bp overlap, no mismatches), filtered for chimeras and dereplicated (pool = TRUE) using the DADA2 package (Callahan et al. 2016) in R (v3.5.3; R Core Team 2015). To maximize biodiversity detections, we retained high-quality singletons (that passed strict quality filtering, denoising, and chimera removal) if they were observed in at least two independent samples (DADA2 Pool=TRUE function). If the singleton was only found in one sample, it was removed from the dataset. This generated an amplicon sequence variant (ASV) .fasta file and count table; the former was queried against NCBI’s GenBank nucleotide database (accessed September 2020; Benson et al. 2005) using BLASTn (minimum percentage identity = 90, maximum target sequences = 10, reward value = 1) with Zeus, an SGI cluster, based at the Pawsey Supercomputing Centre in Kensington, Western Australia. Taxonomic assignments of ASVs were curated and, when necessary, collapsed to the lowest common ancestor (LCA) using a custom LCA python script (Mousavi‐Derazmahalleh et al. 2021), with a threshold query coverage (qCov) of 100%, a minimum percentage identity of 90%, and a difference (Diff) of 1. ASVs detected in extraction blanks with a read count >10 were removed across the entire dataset, prior to ASVs being merged by taxonomy using the phyloseq v1.24.2 ‘tax_glom’ function (McMurdie and Holmes 2013) in R. Sample replicates were then pooled by their temporal sampling period and taxa accumulation curves were plotted by sequencing depth using the vegan v2.5-7 rarecurve function (Oksanen et al. 2019) in R. These rarefaction analyses (Fig. S2 and S3 in Online Resource 1) indicated that subsampling of sequencing depth was not required, given that a plateau was apparent in the taxa accumulation curves.
We here provide the demultiplexed 16S Fish (read 1 only), as well as the Coral ITS2 (CP1) and Coral ITS2_acros (CP2; read 1 and read 2) assay sequence data in .fastq format, along with an excel spreadsheet listing the metadata associated with each seawater sample collected at Lizard Island, Australia. These sequences and metadata were used in the following paper:
DiBattista, J.D., West, K.M., Ceccarelli, D.M., Hoggett, A.K., Vail, L.L., Garcia, R., and Richards, Z.T. (in press) An examination of seasonal variation in taxonomic richness and community composition using eDNA on a tropical coral reef. Coral Reefs. https://doi.org/10.1007/s00338-024-02594-6