PHYLOGENETIC SELECTION OF A RESOURCE: A NEW USE FOR CLADISTICS

A phylogenetic model for the selection of commercial resources using the cladistic method is proposed. The group selected as an example was the marine agarophyte red algal genus Gracilaria Greville. We suggest the use of the cladistic principle of evolutionary transformational series in order to test the quality of agars instead of the assay‐herror traditional method that consumes time and budget. If we asume that the “good quality of agar” in extant taxa is a sinapomorphic character (but not a reliable taxonomic one), then taxa included in the same monophiletic clade in which the species with “good quality of agar” are, has a high evolutionary posibility to share that character. In order to do this we have to incorporate to the set of available specific characters, those of the taxa actually used as a agar source but not present in the area under scope. A complete set of the basic cladistic data required for run the most popular program currently in use (PAUP) are provided. We applied the model to the Mexican Atlantic species and found that, using Gracilaria chilensis and G. cornea as “indicator taxa,” and found Mexican populations of G. crassissima, G. caudata, G. cervicornis and Gracilariopsis lemaneiformis are candidates for a study of yield and agar properties.     

Comparison of three gracilarioids: growth rate, agar content and quality

Three gracilarioid species, Gracilariopsis bailiniae and Gracilaria tenuistipitata from Vietnam and Gracilaria gracilis from Russia, were studied in order to determine whether Gracilaria gracilis might be a superior species for cultivation in brackish-water ponds for agar production compared with the Vietnamese species. The effects of different salinity levels on the growth rate and agar production as well as agar properties of three gracilarioid species were compared in controlled laboratory experiments. Gracilaria tenuistipitata and G. gracilis were tolerant to low salinity (∼10‰), whereas Gp. bailiniae died under these conditions. G. tenuistipitata showed superior growth among the three species examined. Gracilaria gracilis had the highest agar content [36.8–46.6% dry weight (dw)]. Agar yield from Vietnamese gracilarioids did not exceed 30% dw. Gel strength of native agar from Gracilaria gracilis was two-fold higher that from Vietnamese species (278 g cm⁻² vs 130 g cm⁻²). Alkali pretreatment increased gel strength significantly for Gracilaria gracilis (1.4-fold), and G. tenuistipitata and Gp. bailiniae (2.3-fold) compared with native agar. The results suggest that Gracilaria gracilis may be a suitable species for production of reasonably good quality agar.     

COULD A CLADOGRAM THIS SHORT HAVE ARISEN BY CHANCE ALONE?: ON PERMUTATION TESTS FOR CLADISTIC STRUCTURE

Abstract Absolute criteria for evaluating cladistic analyses are useful, not only because cladistic algorithms impose structure, but also because applications of cladistic results demand some assessment of the degree of corroboration of the cladogram. Here, a means of quantitative evaluation is presented based on tree length. The length of the most-parsimonious tree reflects the degree to which the observed characters co-vary such that a single tree topology can explain shared character states among the taxa. This “cladistic covariation” can be quantified by comparing the length of the most parsimonious tree for the observed data set to that found for data sets with random covariation of characters. A random data set is defined as one in which the original number of characters and their character states are maintained, but for each character, the states are randomly reassigned to the taxa. The cladistic permutation tail probability, PTP, is defined as the estimate of the proportion of times that a tree can be found as short or shorter than the original tree. Significant cladistic covariation exists if the PTP is less than a prescribed value, for example, 0.05. In case studies based on molecular and morphological data sets, application of the PTP shows that:

• 1 In the comparison of four different molecular data sets for orders of mammals, the sequence data set for alpha hemoglobin does not have significant cladistic covariation, while that for alpha crystallin is highly significant. However, when each data set was reduced to the 11 common taxa in order to standardize comparison, reduced levels of cladistic covariation, with no clear superiority of the alpha crystallin data, were found. Morphological data for these 11 taxa had a highly significant PTP, producing a tree roughly congruent with those for the three molecular sets with marginal or significant PTP values. Merging of all data sets, with the exclusion of the poorly structured alpha hemoglobin data, produced a data set with a significant PTP, and provides an estimate of the phylogenetic relationships among these 11 orders of mammals.
• 2 In an analysis of lactalbumin and lysozyme DNA sequence data for four taxa, purine-pyrimidine coding yields a data set with significant cladistic covariation, while other codings fail. The data for codon position 3 taken alone exhibit the strongest cladistic covariation.
• 3 A data set based on flavonoids in taxa of Polygonum initially yields a significant PTP; however, deletion of identically scored taxa leaves no significant cladistic covariation.
• 4 For mitochondrial DNA data on population genome types for four species of the crested newt, there is significant cladistic covariation for the set of all genome types, and among the five mtDNA genome types within one of the species. However, a conditional PTP test that assumes species monophyly shows that no significant cladistic covariation exists among the fur species for these data.
• 5 In an application of the test to a group of freshwater insects, as preliminary to biological monitoring, individual subsets of the taxonomic data representing larval, pupal, and adult stages had non-significant PTPs, while the complete data set showed significant cladistic structure.

     

Agars from three species of Gracilaria (Rhodophyta) from Yucatán Peninsula

Gracilaria cervicornis, Gracilaria blodgettii and Gracilaria crassissima growing along the coasts of Yucatán were investigated for their agar content. The effect of different concentrations of NaOH in the alkali treatment was evaluated. The three species of Gracilaria produced agars, both native and alkali treated, with different properties confirming the heterogeneity of the agar polymers in this genera. G. cervicornis produces agar polymers with an occurrence of methoxylation and sulphation at the C-6 of the beta-D-galactose residues, and with an extra methylation due to the presence of the 4-O-methyl-alpha-L-galactose residue. The presences of these residues is responsible for the extremely poor gelling ability of its agarocolloids, whose commercial value seems to be quite low. Agar extracts from G. blodgettii showed the typical pattern of unsubstituted agar with a very low degree of methylation on both galactose residues. The discrepancy found between sulphate content and NMR data of agar from this species requires a more detailed structural investigation. G. crassissima produces a good quality agar after sulphate precursor sequences have been removed by alkaline treatment, and it may be considered for exploitation as a source of commercial grade agar. Alkali treatment was effective both in removing alkali-labile sulphate and increasing the gel strength in G. crassissima but not in G. cervicornis and G. blodgettii.     

PHYLOGENETIC RETICULATIONS AND CLADISTICS: DISCUSSION OF METHODOLOGICAL CONCEPTS

Abstract— Some problems associated with a cladistic treatment of complex taxa (hybrids and holobionts) are reviewed and discussed. The authors recommend aplication of standard cladistic analysis to all taxa, regardless of their supposed mode of origin. The position of a complex taxon depends entirely on the set of characters it shares with other taxa. This approach is preferable, because there are no means to distinguish deductively between various kinds of character conflicts (the recognition of one character as incongruous with others says nothing about its evolutionary origin). All other approaches have been proposed so as to reflect the topology of reticulate phylogenetic trees, but, at the same time, they require prior knowledge of the complex nature of a taxon.     

Growth,photosynthesis and agar in wild-type strains of Gracilaria verrucosa and G. conferta (Gracilariales,Rhodophyta), as a strain selection experiment

The local species Gracilaria conferta and the foreign G. verrucosa were grown together under a wide range of photon flux density and temperature conditions. Gracilaria verrucosa showed a higher growth rate, especially under low temperatures, and higher photosynthetic performances as well as higher ribulose-1,5-bisphosphate carboxylase activity as compared with G. conferta. Gracilaria verrucosa also showed a better quality and yield of agar, suggesting that this species could be more suitable than G. conferta for outdoor cultivation in Israel and may improve winter growth in ponds. Growth rate and agar quality (gel strength) were rated as the most suitable characteristics influencing the preference of strains for outdoor cultivation.     

Agar polysaccharides from Gracilaria species (Rhodophyta, Gracilariaceae)

Yield, physical and chemical properties of agar from three agarophytes species (Gracilaria gracilis, G. dura and G. bursa-pastoris) were determined. The agar yield from the three species varied significantly (P<0.01). The highest yields of agar (34.8%) and the lowest (30%) were obtained from G. bursa-pastoris and G. gracilis, respectively. Highest gel strength (630+/-15 g cm(-2)) was obtained from agar extracted from G. gracilis and lowest from G. bursa-pastoris (26+/-3.6 g cm(-2)). The values of 3,6-anhydrogalactose were similar for G. gracilis and G. dura and there were no significant differences among the species. The sulfate contents varied significantly (P<0.01) and the higher value was obtained from G. bursa-pastoris. Among the three species, G. gracilis showed superior agar quality than the other two species, hence it can be considered a good potential source for industrial use.     

How much can cladistics tell us about early hominid relationships?

Although cladistic analysis has been used to compare hypotheses of relationships among early hominids, the outcomes of different studies have depended entirely on the assumptions made by different investigators. Problems include the close genetic relationship of early hominid taxa, small fossil sample sizes, possible correlations among characters, and a lack of understanding about the evolutionary factors affecting characters. This study investigates the interaction of some of these problems affecting early hominid phylogenetics. Monte Carlo simulations of character state evolution in closely related taxa demonstrate that the sample sizes and close genetic relationships of early hominids do not permit cladistic analyses to obtain unequivocal results. Even with unrealistically good assumptions about the evolutionary dynamics affecting characters, the probability of the most parsimonious hypothesis being true is unacceptably small. In the face of these problems, even phylogenetic statements that are supported by a strong consensus of cladistic studies may nevertheless be in error, and such errors are likely to confound the placement of new specimens and taxa. Advancement in our knowledge of hominid phylogeny can depend only on a fuller understanding of the natural history and evolutionary dynamics of traits.     

HYBRIDS AND PHYLOGENETIC SYSTEMATICS I. PATTERNS OF CHARACTER EXPRESSION IN HYBRIDS AND THEIR IMPLICATIONS FOR CLADISTIC ANALYSIS

Interspecific hybridization is considered common among plants, but the methods of cladistic systematics produce only divergently branching phylogenetic hypotheses and thus cannot give the correct phylogeny if an analysis includes hybrids. Empirical studies of the impact of known hybrids on phylogenetic analysis are lacking, and are necessary to begin to understand the problems that we face if hybrids are often included in cladistic analysis. Examination of the implications of hybrids for cladistics must begin with patterns of character expression in hybrids. This study includes 17 hybrids and their nine parental taxa that are Central American species of Aphelandra (Acanthaceae), analyzed using a set of 50 morphological characters. The hybrids are overwhelmingly intermediate as quantitatively scored for phylogenetic analysis. They express maternal and paternal, and primitive and derived characters in equal frequencies, showing no evidence of predominant inheritance of derived character states as has been assumed by most cladists who have considered hybrids theoretically. Because of their known genetic constitution, hybrids were useful in homology assessment and ordering character states. The parental character set was generally robust, but some changes were made to reflect the special evidence offered by the hybrids. These hybrids suggest that the inclusion of hybrids in phylogenetic analysis will not lead to unresolved cladograms with rampant homoplasy, as has been predicted by other authors. Instead, the patterns of character inheritance in these hybrids lead to the prediction that a hybrid will be placed by phylogenetic analysis as a basal lineage to the clade that includes its most derived parent, with relatively little effect on homoplasy. These predictions will be evaluated by incorporation of the hybrids in phylogenetic analyses, to be reported in a subsequent paper.     

Phylogeny reconstruction in the neogene bryozoan metrarabdotos: A paleontologic evaluation of methodology

An adequate stratigraphic record can not only aid in both cladistic and stratophenetic reconstruction of phytogenies, but can also serve in estimating the temporal consistency of the resulting phylogenetic trees. For hypothetical data sets, cladistically constructed trees can be as consistent with the temporal distribution of sampled populations or species as those constructed stratophenetically. Empirical testing in taxonomic groups with sufficiently dense fossil records is needed to show whether, and under what conditions, this potential can be realized. A stratophenetic tree and cladistic trees based on several approaches to character weighting were constructed for Caribbean Neogene species of the bryozoan Metrarabdotos with multiple‐character data from closely spaced sequential populations. The modular morphology and highly punctuated evolutionary pattern of these species blur the distinction between continuous and discrete characters, so that all available characters are potentially of equal significance in establishing phytogenies, rather than just those with discrete states conventionally used in cladistic analysis. However, only the cladistic trees generated with all characters weighted to emphasize contribution to species discrimination have temporal consistencies that are clearly significant statistically and approach that of the stratophenetic tree in magnitude. These results provide a start toward establishing general guidelines for cladistic analysis of taxa with stratigraphie records too sparse for stratophenetic reconstruction.     

Information obtained in cladistic analysis.

The application of elementary equations from information theory to the elements involved in cladistic analysis is formalized mathematically. An equation is derived that quantifies the amount of information obtained by constructing a cladogram from a cladistic data matrix. Given particular conditions, the amount of information obtained increases monotonically with increases of the number of taxa involved and, so, may be used directly as a comparative measure of species richness for sister groups; in general, however, the amount of information obtained is related to the distribution of character states on the cladogram(s) deduced. An example is presented in which clades representing 11 phyla in the animal kingdom are compared in terms of information yielded. The amount of information obtained is consistent for different numbers of taxa and characters used in classifications. Speculative evolutionary explanations are presented for differences of information yielded among the phyla analyzed.     

Seasonal variation of the agar quality and chemical composition of Gracilaria veleroae and Gracilaria vermiculophylla (Rhodophyceae,Gracilariaceae) from Baja California Sur,Mexico

Yield and physico‐chemical properties of agar from Gracilaria veleroae E.Y. Dawson and Gracilaria vermiculophylla (Ohmi) Papenfuss were studied and the chemical composition of the two seaweeds was determined. Samples were collected seasonally from summer 2003 to spring 2005. The agar yield did not vary significantly between seasons for both species. The lowest agar gel strength was obtained from G. veleroae (207.5 g cm^–2) in summer 2003 and the highest from G. vermiculophylla (793.1 g cm^–2) in winter 2004. Melting temperatures and hysteresis were higher in G. vermiculophylla, whereas gelling temperatures and 3,6‐anhydrogalactose content were higher for G. veleroae. Moisture, ash, crude fiber, and ether extract showed no significant seasonal variation for G. veleroae. The chemical composition of G. vermiculophylla showed significant seasonal variation. G. vermiculophylla possesses a better agar quality than G. veleroae and is a species that could be considered as a source of agar for commercial use.     

Paraphyly,ancestors, and the goals of taxonomy: A botanical defense of cladism

Cronquist (1987) criticizes cladism for its rejection of paraphyletic groups, which he would retain if he feels they are “conceptually useful.” We argue that paraphyletic higher taxa are artificial classes created by taxonomists who wish to emphasize particular characters or phenetic “gaps,” and that formal recognition of such taxa conveys a misleading picture of common ancestry and character evolution. In our view, classifications should accurately reflect the nested hierarchy of monophyletic groups that is the natural outcome of the evolutionary process. Such systems facilitate the study of evolution and provide an efficient summary of character distributions. Paraphyletic groups, such as “prokaryotes,” “green algae,” “bryophytes,” and “gymnosperms,” should be abandoned, as continued recognition of such groups will only serve to retard progress in understanding evolution. Contrary to Cronquist’s (1987) assertions, cladistic theory is not at odds with standard views on speciation and the existence of ancestors. Groups of interbreeding organisms can continue to exist after giving rise to descendant species, and there are several ways in which such groups, whether extant or extinct, can be incorporated into cladistic classification. In contrast, paraphyletic higher taxa are neither cohesive (integrated by gene flow) nor whole, do not serve as ancestors, and are unacceptable in the phylogenetic system. Fossils may be of great value in assessing phylogenetic relationships and are readily accommodated in cladistic classification. Cladistic studies are helping to answer major questions about plant evolution, and we anticipate increased efforts to develop a truly phylogenetic system.     

POLYMORPHIC TAXA, MISSING VALUES AND CLADISTIC ANALYSIS

Abstract Missing values have been used in cladistic analyses when data are unavailable, inapplicable or sometimes when character states are variable within terminal taxa. The practice of scoring taxa as having "missing values" for polymorphic characters introduces errors into the calculation of cladogram lengths and consistency indices because some character change is hidden within terminals. Because these hidden character steps are not counted, the set of most parsimonious cladograms may differ from those that would be found if polymorphic taxa had been broken into monomorphic subunits. In some cases, the trees found when polymorphisms are scored as missing values may not include any of the most parsimonious trees found when the data are scored properly. Additionally, in some cases, polymorphic taxa may be found to be polyphyletic when broken into monomorphic subunits; this is undetected when polymorphisms are treated as missing. Because of these problems, terminal units in cladistic analysis should be based on unique, fixed combinations of characters. Polymorphic taxa should be subdivided into subunits that are monomorphic for each character used in the analysis. Disregarding errors in topology, the additional hidden steps in a cladogram in which polymorphisms are scored as missing can be calculated by a simple formula, based on the observation that if it is assumed that polymorphic terminals include all combinations of character states, 2 ^p − 1 additional steps are required for each taxon in which p polymorphic binary characters are scored as missing values. Thus, when several polymorphisms are scored as missing in the same taxon, very large errors can be introduced into the calculation of tree length.     

DEFENSE EVOLUTION IN THE GRACILARIACEAE (RHODOPHYTA): SUBSTRATE‐REGULATED OXIDATION OF AGAR OLIGOSACCHARIDES IS MORE ANCIENT THAN THE OLIGOAGAR‐ACTIVATED OXIDATIVE BURST1

Combined phylogenetic, physiological, and biochemical approaches revealed that differences in defense‐related responses among 17 species belonging to the Gracilariaceae were consistent with their evolutionary history. An oxidative burst response resulting from activation of NADPH oxidase was always observed in two of the subgenera of Gracilaria sensu lato (Gracilaria, Hydropuntia), but not in Gracilariopsis and in species related to Gracilaria chilensis (“chilensis” clade). On the other hand, all species examined except Gracilaria tenuistipitata var. liui and Gracilariopsis longissima responded with up‐regulation of agar oligosaccharide oxidase to an challenge with agar oligosaccharides. As indicated by pharmacological experiments conducted with Gracilaria chilensis and Gracilaria sp. “dura,” the up‐regulation of agar oligosaccharide oxidase involved an NAD(P)H‐dependent signaling pathway, but not kinase activity. By contrast, the activation of NADPH oxidase requires protein phosphorylation. Both responses are therefore independent, and the agar oligosaccharide‐activated oxidative burst evolved after the capacity to oxidize agar oligosaccharide, probably providing additional defensive capacity to the most recently differentiated clades of Gracilariaceae. As demonstrated with Gracilaria gracilis, Gracilaria dura, and Gracilariopsis longissima, the different responses to agar oligosaccharides allow for a fast and nondestructive distinction among different clades of gracilarioids that are morphologically convergent. Based upon sequences of the chloroplast‐encoded rbcL gene, this study suggests that at least some of the samples from NW America recorded as Gs. lemanaeiformis are probably Gs. chorda. Moreover, previous records of Gracilaria conferta from Israel are shown to be based upon misidentification of Gracilaria sp. “dura,” a species that belongs to the Hydropuntia subgenus.     

Problems with the use of cladistic analysis in palaeoanthropology

Cladistic analysis is a popular method for reconstructing evolutionary relationships on the human lineage. However, it has limitations and hidden assumptions that are often not considered by palaeoanthropologists. Some researchers who are opposed to its use regard cladistics as the preferred method for taxonomic «splitters» and claim it has lead to a revitalisation of typology. Typology remains a part of human evolutionary studies, regardless of the acceptance or use of cladistics. The assumption/preference for «splitting» over «lumping» in cladistics (alpha) taxonomy and the general failure to evaluate (post-hoc) such taxonomies have served to reinforce this assertion.

Researchers have also adopted a number of practices that are logically untenable or introduce considerable error. The evolutionary trend of human encephalisation, apparently isometric with body size, and concurrent reduction in the gut and masticatory apparatus, suggests continuous cladistic characters are biased by problems of body size.

The method suffers a logical weakness, or circularity, leading to bias when characters with multiple states are used. Coding of such characters can only be done using prior criteria, and this is usually done using an existing phylogenetic scheme. Another problem with coding character states is the handling of variation within species. While this form of variation is usually ignored by palaeoanthropologists, when characters are recognised as varying, their treatment as a separate state adds considerable error to cladograms.

The genetic proximity of humans, chimpanzees and gorillas has important implications for cladistic analyses. It is argued that chimpanzees and gorillas should be treated as ingroup taxa and an alternative outgroup such as orangutans should be used, or an (hypothetical) ancestral body plan developed. Making chimpanzees and gorillas ingroup taxa would considerably enhance the biological utility of anthropological cladograms.

All published human cladograms fail to meet standard quality criteria indicating that none of them may be considered reliable. The continuing uncertainty over the number and composition of fossil human species is the largest single source of error for cladistics and human phylogenetic reconstruction.     

Escaping from the Felsenstein Zone by Detecting Long Branches in Phylogenetic Data

Long branches in a true phylogeny tend to disrupt hierarchical character covariation (phylogenetic signal) in the distribution of traits among organisms. The distortion of hierarchical structure in character-state matrices can lead to errors in the estimation of phylogenetic relationships and inconsistency of methods of phylogenetic inference. Examination of trees distorted by long-branch attraction will not reveal the identities of problematic taxa, in part because the distortion can mask long branches by reducing inferred branch lengths and through errors in branching order. Here we present a simple method for the detection of taxa whose placement in evolutionary trees is made difficult by the effects of long-branch attraction. The method is an extension of a tree-independent conceptual framework of phylogenetic data exploration (RASA). Taxa that are likely to attract are revealed because long branches leave distinct footprints in the distribution of character states among taxa, and these traces can be directly observed in the error structure of the RASA regression. Problematic taxa are identified using a new diagnostic plot called the taxon variance plot, in which the apparent cladistic and phenetic variances contributed by individual taxa are compared. The procedure for identifying long edges employs algorithms solved in polynomial time and can be applied to morphological, molecular, and mixed characters. The efficacy of the method is demonstrated using simulated evolution and empirical evidence of long branches in a set of recently published sequences. We show that the accuracy of evolutionary trees can be improved by detecting and combating the potentially misleading influences of long-branch taxa.     

Mapping cladograms into morphospaces

In cladistic analyses, taxa are grouped hierarchically into clades according to shared apomorphic character states to construct cladograms; cladograms are interpretable as phylogenetic hypotheses. In morphological space analyses, organism forms are represented as points in morphospaces; point proximities in morphospaces represent similarities that might be attributable to phenetic convergence and, consequently, may correspond inaccurately with hypothesized evolutionary relationships. A method for synthesizing phylogenetic results that are interpreted from cladistic analyses with phenetic results that are obtained from morphological space analyses is presented here; in particular, points that represent forms typifying taxa in morphospace are assigned as terminal nodes for appropriate cladograms that are mapped into morphospaces by positioning nonterminal nodes and orienting internodes according to a geometric algorithm. Nonterminal nodes may be interpreted as ancestors in phylogenetic hypotheses and occupy positions that represent particular organism forms in morphospaces. By mapping cladograms into morphospaces, therefore, evolutionary morphologists can reconstruct ancestral morphologies and test historical transformation hypotheses.     

Phylogeny of Trichomonads Based On Partial Sequences of Large Subunit Rrna and On Cladistic Analysis of Morphological Data

ABSTRACT. Several domains of large subunit rRNA from nine trichomonad species have been sequenced. Molecular phylogenies obtained with parsimony and distance methods demonstrate the trichomonads are a monophyletic group which branches very early in the eukaryotic tree. the topology of the trees is in general agreement with traditional views on evolutionary and systematic relationships of trichomonads. A clear dichotomy is noted between the subfamily Trichomonadinae and the subfamily Tritrichomonadinae. In the latter subfamily, a second division separates the " Tritrichomonas muris -type" species from the " Tritrichomonas augusta -type" ones. Previous evolutionary schemes in which the Monocercomonadidae were regarded as the most "primitive" and the Trichomonadidae as more "evolved" are not in agreement with our molecular data. the emergence of Monocercomonas and Hypotrichomonas at the base of the Tritrichomonas lineage suggests a secondary loss of some cytoskeletal structures, the costa and undulating membrane in these genera. This is corroborated by the early branching position of Trichomitus. which possesses a costa and an undulating membrane and has usually been placed among the Trichomonadidae on the basis of cytological characters. A cladistic analysis was applied to the available morphological characters in order to produce a hierarchical grouping of the taxa reflecting their morphological diversity. Supplementary key words. Evolution, molecular phylogeny, morphological cladistic analysis.