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Species Variability and Connectivity in the Deep Sea: Evaluating Effects of Spatial Heterogeneity and Hydrodynamic Effects] Supplementary material for [L Lins], [2016], [Species variability and connectivity in the deep sea: evaluating effects of spatial heterogeneity and hydrodynamic effects] Species variability and connectivity in the deep sea: evaluating effects of spatial heterogeneity and hydrodynamic effects Supplementary material for [L Lins], [2016], [Species variability and connectivity in the deep sea: evaluating effects of spatial heterogeneity and hydrodynamic effects] Supplementary material for [L Lins], [2016], [Species variability and connectivity in the deep sea: evaluating effects of spatial heterogeneity and hydrodynamic effects] Supplementary Figure 1: Partial-18S rDNA phylogeny of Nematoda: Chromadorea. The inferred relationships support a broad taxonomic representation of nematodes in samples from lower shelf and upper slope at the West-Iberian Margin and furthermore indicate neither geographic nor depth clustering between ‘deep’ and ‘shallow’ taxa at any level of the tree topology. Reconstruction of nematode 18S relationships was conducted using Maximum Likelihood. Bootstrap support values were generated using 1000 replicates and are presented as node support. The analyses were performed by means of Randomized Axelerated Maximum Likelihood (RAxML). Branch (line) width represents statistical support. Sequences retrieved from Genbank are represented by their Genbank Accession numbers. Orders and Families are annotated as branch labels. PERMANOVA table of results (2-factor design) Source df SS MS Pseudo-F P(perm) Unique perms Depth 1 105.29 105.29 18,037 0.0027 3014 Station(Depth) 8 45,042 56,302 28,113 0.0001 9929 Res 22 4,406 0.20027 Total 31 155 PAIR-WISE TESTS Term 'Station(Depth)' Within level 'DEEP' of factor 'Depth' Groups t Unique perms P(MC) D1, D2 14,453 35 0.1836 D1, D3 0.21922 35 0.9692 D1, D4 11,404 35 0.2898 D2, D3 28,189 35 0.0062 D2, D4 0.74526 35 0.5423 D3, D4 17,462 35 0.0754 Within level 'SHALLOW' of factor 'Depth' Groups t Unique perms P(MC) Supplementary material for [L Lins], [2016], [Species variability and connectivity in the deep sea: evaluating effects of spatial heterogeneity and hydrodynamic effects] S1, S4 52,363 10 0.005 S1, S7 14,786 10 0.0004 S1, S2 59,548 10 0.0019 S1, S614 54,457 10 0.0094 S1, S613 10,274 10 0.0004 S4, S7 15,104 10 0.0009 S4, S2 72,374 10 0.0008 S4, S614 7.09 10 0.0027 S4, S613 12,505 10 0.0002 S7, S2 27,661 10 0.0586 S7, S614 41,579 3 0.036 S7, S613 61,604 10 0.0049 S2, S614 10,659 10 0.3696 S2, S613 0.80935 10 0.4851 S614, S613 0.81016 10 0.4904 Supplementary Table 1: Table of results from the multivariate PERMANOVA two-way nested design test and pairwise t-tests for sediment composition. Values in bold represent significant values. PERMANOVA table of results (2-factor design) Unique Source df SS MS Pseudo-F P(perm) perms Depth 1 28,266 28,266 290.31 0.0038 3009 Station(Depth) 8 0.75128 9.39E+01 13,912 0.2576 9951 Res 22 14,851 6.75E+02 Total 31 31 PAIR-WISE TESTS Within level 'DEEP' of factor 'Depth' Unique Groups t perms P(MC) D1, D2 0.87706 35 0.4193 D1, D3 21,165 35 0.0767 D1, D4 15,794 35 0.1669 D2, D3 12,268 35 0.28 D2, D4 0.4402 35 0.6771 D3, D4 0.94545 35 0.3727 Supplementary material for [L Lins], [2016], [Species variability and connectivity in the deep sea: evaluating effects of spatial heterogeneity and hydrodynamic effects] Within level 'SHALLOW' of factor 'Depth' Unique Groups t perms P(MC) S1, S4 11,198 10 0.0006 S1, S7 38,705 10 0.0297 S1, S2 11,958 10 0.2967 S1, S614 0.69613 10 0.5416 S1, S613 10,709 10 0.3462 S4, S7 12,439 10 0.0016 S4, S2 59,381 10 0.0047 S4, S614 36,069 10 0.0393 S4, S613 81,676 10 0.0015 S7, S2 12,966 10 0.2842 S7, S614 0.7778 3 0.5125 S7, S613 21,078 10 0.1247 S2, S614 4.62E+02 10 0.9641 S2, S613 0.2926 10 0.7909 S614, S613 0.13656 10 0.8965 Supplementary Table 2: Table of results from the multivariate PERMANOVA two-way nested design test and pairwise t-tests for Total Organic Matter (%). Values in bold represent significant values. PERMANOVA table of results (2-factor design) Unique Source df SS MS Pseudo-F P(perm) perms Depth 1 26,291 26,291 117.4 0.0044 2982 Station(Depth) 8 1,728 0.216 2.1723 0 9948 Res 22 2.1876 9.94E+02 Total 31 31 PAIR-WISE TESTS Term 'Station(Depth)' Within level 'DEEP' of factor 'Depth' Unique Groups t perms P(MC) D1, D2 6.24E+02 35 0.9543 D1, D3 14,616 35 0.1973 D1, D4 16,115 35 0.1581 D2, D3 14,857 35 0.1932 Supplementary material for [L Lins], [2016], [Species variability and connectivity in the deep sea: evaluating effects of spatial heterogeneity and hydrodynamic effects] D2, D4 16,355 35 0.1534 D3, D4 0.52802 35 0.6108 Within level 'SHALLOW' of factor 'Depth' Unique Groups t perms P(MC) S1, S4 43,932 10 0.0127 S1, S7 4.85E+02 10 0.9671 S1, S2 13,419 10 0.2507 S1, S614 2,617 10 0.0761 S1, S613 25,712 10 0.0639 S4, S7 21,765 10 0.1079 S4, S2 42,708 10 0.0127 S4, S614 20,996 10 0.1254 S4, S613 65,162 10 0.0032 S7, S2 0.85525 10 0.4589 S7, S614 0.97067 3 0.4387 S7, S613 13,943 10 0.2571 S2, S614 25,694 10 0.0814 S2, S613 0.49958 10 0.6447 S614, S613 47,643 10 0.0171 Supplementary Table 3: Table of results from the multivariate PERMANOVA two-way nested design test and pairwise t-tests for Total Organic Carbon (%). Values in bold represent significant values. PERMANOVA table of results (2-factor design) Unique Source df SS MS Pseudo-F P(perm) perms Depth 1 24,328 24,328 68.19 0.0031 2975 Station(Depth) 8 27,534 0.34417 1.7061 0.1482 9942 Res 22 4.4381 0.20173 Total 31 31 PAIR-WISE TESTS Term 'Station(Depth)' Within level 'DEEP' of factor 'Depth' Unique Groups t perms P(MC) D1, D2 0.23752 35 0.8173 D1, D3 25,534 35 0.0417 D1, D4 0.91472 35 0.3884 D2, D3 11,073 35 0.3213 Supplementary material for [L Lins], [2016], [Species variability and connectivity in the deep sea: evaluating effects of spatial heterogeneity and hydrodynamic effects] D2, D4 0.34137 35 0.7475 D3, D4 11,913 35 0.2853 Within level 'SHALLOW' of factor 'Depth' Unique Groups t perms P(MC) S1, S4 69,773 10 0.0027 S1, S7 0.721 10 0.517 S1, S2 0.64104 10 0.5577 S1, S614 0.31006 10 0.7737 S1, S613 2,198 10 0.0896 S4, S7 59,241 10 0.0097 S4, S2 29,036 10 0.0415 S4, S614 24,086 10 0.0942 S4, S613 1.21 10 0.2871 S7, S2 0.91122 10 0.4207 S7, S614 0.53866 3 0.6433 S7, S613 20,931 10 0.1266 S2, S614 0.14015 10 0.9037 S2, S613 12,206 10 0.2896 S614, S613 10,775 10 0.356 Supplementary Table 4: Table of results from the multivariate PERMANOVA two-way nested design test and pairwise t-tests for Total Nitrogen (%). Values in bold represent significant values. PERMANOVA table of results (2-factor design) Unique Source df SS MS Pseudo-F P(perm) perms Depth 1 13,669 13,669 1,149 0.3532 3010 Station(Depth) 8 93,176 11,647 12,613 0.246 9929 Res 22 20,316 0.92343 Total 31 31 PAIR-WISE TESTS Term 'Station(Depth)' Within level 'DEEP' of factor 'Depth' Unique Groups t perms P(MC) D1, D2 10,171 15 0.3465 D1, D3 0.51803 4 0.6248 D1, D4 0.1894 8 0.8526 D2, D3 14,632 8 0.19 D2, D4 0.74632 15 0.4868 D3, D4 0.63864 4 0.542 Supplementary material for [L Lins], [2016], [Species variability and connectivity in the deep sea: evaluating effects of spatial heterogeneity and hydrodynamic effects] Within level 'SHALLOW' of factor 'Depth' Unique Groups t perms P(MC) S1, S4 11,913 2 0.2925 S1, S7 51,545 4 0.0146 S1, S2 1 1 0.3738 S1, S614 12,399 4 0.0006 S1, S613 36,177 4 0.0248 S4, S7 0.82471 10 0.4677 S4, S2 11,092 4 0.3355 S4, S614 0.77009 10 0.5019 S4, S613 0.74004 10 0.4872 S7, S2 0.45648 7 0.676 S7, S614 1,801 3 0.2177 S7, S613 19,838 10 0.1387 S2, S614 11,506 7 0.333 S2, S613 2.51 7 0.0646 S614, S613 15,554 10 0.2141 Supplementary Table 5: Table of results from the multivariate PERMANOVA two-way nested design test and pairwise t-tests for Chlorophyll a (µg/g). Values in bold represent significant values. PERMANOVA table of results (2-factor design) Unique Source df SS MS Pseudo-F P(perm) perms P(MC) Depth 1 80,288 80,288 33,462 72 0.1063 Station(Depth) 8 17,986 22,482 99,215 0.0028 9931 Res 22 49,853 0.2266 Total 31 31 PAIR-WISE TESTS Within level 'DEEP' of factor 'Depth' Groups t Denominator D1, D2 is 0 Denominator D1, D3 is 0 Denominator D1, D4 is 0 Denominator D2, D3 is 0 Denominator D2, D4 is 0 Denominator D3, D4 is 0 Within level 'SHALLOW' of factor 'Depth' Supplementary material for [L Lins], [2016], [Species variability and connectivity in the deep sea: evaluating effects of spatial heterogeneity and hydrodynamic effects] Unique Groups t perms P(MC) S1, S4 3,064 10 0.0351 S1, S7 82,415 7 0.0033 S1, S2 0.56826 10 0.6091 S1, S614 82,415 7 0.0031 S1, S613 15,569 10 0.1936 S4, S7 2,905 7 0.0624 S4, S2 27,014 10 0.0544 S4, S614 2,905 7 0.0602 S4, S613 24,855 10 0.0661 S7, S2 1,935 7 0.149 Denominator S7, S614 is 0 S7, S613 29,953 7 0.0617 S2, S614 1,935 7 0.1473 S2, S613 0.58587 10 0.584 S614, S613 29,953 7 0.0583 Supplementary Table 6: Table of results from the multivariate PERMANOVA two-way nested design test and pairwise t-tests for Carotenes (µg/g).
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