Southern California Bight 2003 Regional Monitoring Program: IV. Demersal Fishes and Megabenthic Invertebrates
Parsimony analysis of Combined Fish and invertebrate Clades
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- Figure VI-14. Distribution of demersal fish and megabenthic invertebrate site cluster on the southern California shelf and upper slope at depths of 2-476 m, July-October 2003.
- Station Groupings.
Parsimony analysis of Combined Fish and invertebrate CladesDiversity Analyses. With such a large data set, patterns in matrices of diversity analyses were difficult to discern or summarize (Appendix D-D12). However, Mesquite (a recently developed and sophisticated software; Maddison and Maddison 2004) software allowed employment of mapping modules that literally illuminate these continuous values over and through the cladogram. Species richness or the total number of species or taxa represented by (S) was captured both via inspection of the length of the branches on the cladogram and by mapping. The highest number of taxa or species richness values were found at the stations with the longest branches, namely Stations 4235 and 4029, followed by 4256, 4258, and 4096. In general, the shallower stations possessed fewer numbers of species than the remaining groups. No real patterns emerge regarding abundance values with the exception of extremely high values found at deep outer shelf Stations 4179 (364 m) and 4091 (428 m) due to very high collections of northern heart urchin and northern heart urchin plus the sea star Myxoderma platyacanthum, respectively. The pattern of Margalef’s index “d” generally mirrored that seen with the total number of species (S). Pielou’s evenness (J’) showed highest values in the shallow bays and harbors subclade composed of mainly marina samples bordered by stations 4065 and 4204 on the cladogram (Figure VI-15). The Shannon-Wiener index of diversity (H’) tended to produce higher values in the two clades located on the middle shelf containing many of the large POTW stations. Simpson’s dominance (1-lambda) showed rather high scores throughout the samples with the general pattern mirroring Pielou’s evenness (d’). Although conventional biodiversity indices are presented in Appendix D-D12, the series of new biodiversity measures presented here more accurately reflect taxonomic, and ideally, phylogenetic relationships. The suite of taxonomic distinctness and phylogenetic diversity indices were calculated in Primer v5.2.9. These measures include taxonomic diversity (), quantitative taxonomic distinctness (*), average taxonomic distinctness (+), variation in taxonomic distinctness (+), total phylogenetic diversity (S+), and average phylogenetic diversity (+). .Most of these measures have gained immediate acceptance in much of the scientific community in recent years since inception due to their favorable features of being independent of sampling effort, relative to those indices previously employed, and their ability to utilize phylogenetic relationships. These concepts and calculations are presented in Clarke and Warwick (1999), Warwick and Clarke (1995), and Magurran (1988). 
Figure VI-14. Distribution of demersal fish and megabenthic invertebrate site cluster on the southern California shelf and upper slope at depths of 2-476 m, July-October 2003. Assuming taxonomy reflects phylogeny, which recent systematists have striven to achieve with more confidence through advances in technology (i.e., molecular analyses) and cladistics, a sample having five species of the same genus is less biodiverse than another having five species of differing families. Accepting this to be true, indices integrating both taxonomic distances through a tree as well as abundances captures much more information than those traditional indices, and yet most are more robust with respect to independence of samples size/effort. Taxonomic diversity () accomplishes these goals by calculating the expected path length between any two individuals chosen at random. Quantitative taxonomic distinctness (*) still captures the phylogenetic relationships, but on the other hand, removes the influence of dominating abundances to produce an index more reflective of taxonomic hierarchy. This is achieved by dividing () by the Simpson index. Average taxonomic distinctness (+) is merely the taxonomic breadth of a sample event based on presence/absence. This index is most appealing for data with highly variable or unknown sample size and effort. Total taxonomic distinctness (S+) utilizing presence/absence data is the average taxonomic distance from species to species, and is a useful measure of the total taxonomic breadth of an assemblage; hence an assemblage of 20 closely-related species would be calculated to be less diverse than an assemblage of 10 distantly-related species. Variation in taxonomic distinctness (+) can elicit differences among samples having the same + but different taxonomic or phylogenetic tree constructions by focus on the variance of the taxonomic distances between each pair of species about their + value. Total phylogenetic diversity (S+) offers comparison of samples based on cumulative branch lengths of their full trees. This measure is incapable of discriminating samples of equal tree length but differential taxonomic distributions within. Average phylogenetic diversity (+), based on presence/absence data and being the quotient of S+/S, is the contribution that each species makes on the total tree length. As species numbers increase, the later two indices values change noticeably rendering them sample-size/effort dependent. Mapping the aforementioned phylodiversity indices back onto the cladogram (not shown herein, but available from CLAEMD upon request) showed that the general pattern for both total phylogenetic diversity and total taxonomic distinctness mirror the pattern seen with the total number of species (S) very closely. Higher average phylogenetic diversity values were seen in the 2-7 m marina clade and the upper slope clade (Figure VI-15). Average taxonomic distinctness values were generally higher in the 2-7 m marina clade and in the deeper upper slope clade and Channel Island clade; lower values in the variation in taxonomic distinctness also occurred in these three aforementioned clades. Station Groupings. The most parsimonious reconstruction of the combined fish and invertebrate data resulted in a cladogram with a tree length of 2233, a consistency index of 0.225 (maximal value 1.0), and a retention index, which is a measure of branch support, of 0.4417 (maximal value 1.0). The topology of the cladogram (Figure VI-15) reveals several readily identifiable groups or station clades distinguished by depth as well as by predetermined shelf and subshelf zones (strata). In addition, since cladograms are additive trees, branch lengths are indicative of species diversity or the number of species found in a given sample. Thus, providing an additional dimension of information not available in the conventionally used ultrametric trees derived from overall similarity measures in phenetic approaches. 
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