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Chapter 3 - Benthic HabitatsTable 3-2. Distribution of the benthic grab samples by decade and subregion.DecadeGulf of MaineSouthern NewEnglandMid-AtlanticOutside ofregionGrand TotalPre-1950 38 33 2 1 741950s 2,150 660 61 164 3,0351960s 4,146 2,693 857 669 8,3651970s 188 3,770 1,166 4 5,1281980s 637 3,681 1,535 1 5,8541990s 25 25Total 7,159 10,837 3,646 839 22,481Classification MethodsClassification analysis began with the entire 22,481 seafloorsamples taken between 1881 and 1992. However,only about half of the samples contained information onthe full composition or the sample identified to species,and it is that subset of 11,132 samples that is used in thisanalysis. Initially, two separate classifications were created- one based on genera and one based on species as a way ofincluding more samples in the analysis. However, becausethe species level classification showed a stronger relationshipwith the physical factors, this level of taxonomy wasused. Organisms in the samples that were identified onlyto family or order were omitted from the dataset, as werefish, plants, egg masses, and organic debris.Separate classifications were created for each of the threesubregions: the Gulf of Maine, Southern New England,and the Mid-Atlantic Bight (Figure 3-2). For each,samples with similar species composition and abundancewere grouped together using hierarchical cluster analysis(PCORD, McCune and Grace 2002). This techniquestarts with pairwise contrasts of every sample combinationthen aggregates the pairs most similar in species compositioninto a cluster. Next, it repeats the pairwise contrasts,treating the clusters as if they were single samples, andjoins the next most similar sample to the existing clusters.The process is repeated until all samples are assigned toone of the many clusters. For our analysis, the Sorensonsimilarity index and the flexible beta linkage techniquewith Beta set at 25 was used as the basis for measuringsimilarity (McCune and Grace 2002). After groupingthe samples, indicator species analysis was used to identifythose species that were faithful and exclusive to eachorganism group (Dufrene and Legrande 1997). Lastly,Monte Carlo tests of significance were run for each speciesrelative to the organism groups to identify diagnosticspecies for each group using the criterion of a p-value lessthan or equal to 0.10 (90% probability). The number ofsets of clusters (testing 10 to 40) was determined by seeingwhich amount gave the lowest average p-value. Thetest concluded that 20-22 organism groups for each subregionyielded the lowest p-value.Physical Factors: Bathymetry, Substrate andSeabed FormsTo understand how the benthic invertebrate communitydistributions related to the distribution of physical factors,a spatially comprehensive data layer for each factor ofinterest was developed. Four aspects of seafloor structurewere used: bathymetry, sediment grain size, topographicforms, and habitat complexity. These factors were chosenas they are both correlated with the distribution andabundance of benthic organisms (Table 3-1) and are relativelystable over time and space. Variables that fluctuatemarkedly over time were purposely avoided, such astemperature and salinity. Data on each physical factorNorthwest Atlantic Marine Ecoregional Assessment • Phase 1 Report 3-