A numerical analysis of isoelectric focused keratin monomers: Affinities of some western indian ocean green geckos

This is a case study in the numerical analysis of intra- and interspecific differences in isoelectric focused proteins. The proteins are epidermal keratin monomers extracted and characterized by relatively novel porocedures. The numerical analysis of the biochemical data by principal component analysis indicates the relatives similarity of the populations whilst Wagner trees were computed to hypothesize their phylogeny. The character states of the tree nodes (‘ancestors’) are deduced and the phylgenetic tree is fitted directly onto the ordination diagram. In this way evolutionary divargence, convergence and extent of change can be readily visualize. Little convergence exists in this biochemical data set, there being close agreement between the phenetic and phylogenetic analyses. The existence of three species is indicated and this contradicts some facets of the conventional classification.     

Morphological evolution in the day gecko Phelsuma sundbergi in the Seychelles: a multivariate study

Geographic variation was investigated in populations of the day gecko Phelsuma sundbergi from 22 islands in the Seychelles, using multivariate ordination procedures. Multiple group principal components analysis was used to negate ontogenetic variation. Seventy-eight characters from three character systems (body proportions, scalation and colour pattern) were analysed from 349 specimens. Three phenetic aggregations of granitic island populations were detected from the northwestern, northeastern and southern island groups. A comparison of the results from the three character systems analysed separately suggests that the separation of the southern form preceded that of the northern forms. Colour pattern characters reflect this closely, while body proportions and scalation characters follow evolution of body size. The populations of Phelsuma sundbergi on the coralline islands are not well differentiated from the races on the granitic islands, and probably represent recent colonizations or introductions by man.     

Relations phylogénétiques chez les marchantiales (Hepaticae). Incongruence apparente entre données morphologiques et moléculaires

A cladistic analysis of the order Marchantiales based on morphological characters (43 characters) did not agree with the classification in current use. Molecular sequences of nuclear-encoded 26S rRNA genes of seven species of the order and two out-groups (1254–1299 bp) were analysed to solve this contradiction. Results between morphologial and sequence data are conflicting. The combination of the two data sets shows that a weighting of the morphological data corresponding to equal contributions of the two sets resolves contradiction. We demonstrate that the structure of two data sets can be compatible even if the resultant trees are incongruent. Addition of a few compatible data (for instance, via character weighting) can result in congruent trees. The taxonomic incongruence we observed could illustrate a case of too limited molecular sampling.     

Major lineages within Apiaceae subfamily Apioideae: a comparison of chloroplast restriction site and DNA sequence data

Traditional sources of taxonomic characters in the large and taxonomically complex subfamily Apioideae (Apiaceae) have been confounding and no classification system of the subfamily has been widely accepted. A restriction site analysis of the chloroplast genome from 78 representatives of Apioideae and related groups provided a data matrix of 990 variable characters (750 of which were potentially parsimony-informative). A comparison of these data to that of three recent DNA sequencing studies of Apioideae (based on ITS, rpoCl intron, and matK sequences) shows that the restriction site analysis provides 2.6–3.6 times more variable characters for a comparable group of taxa. Moreover, levels of divergence appear to be well suited to studies at the subfamilial and tribal levels of Apiaceae. Cladistic and phenetic analyses of the restriction site data yielded trees that are visually congruent to those derived from the other recent molecular studies. On the basis of these comparisons, six lineages and one paraphyletic grade are provisionally recognized as informal groups. These groups can serve as the starting point for future, more intensive studies of the subfamily.     

Cladistic and phenetic analysis of allozyme data for nine species of sea anemones of the family Actiniidae (Cnidaria: Anthozoa)

The aim of this study was to infer from allozyme data the phylogenetic relationships of nine species of actiniid sea anemones, and also use these data to assess the various methods (phenetic and cladistic) available for phylogenetic analysis. Starch gel electrophoresis was used to obtain genetic data from 13 gene loci. The anemone Metridium senile, from the family Metridiidae, was used as an outgroup. For the phenetic analysis a matrix of pairwise unbiased genetic distances was computed and, from this, dendrograms were produced both by the Wagner distance and the UPGMA methods. For the cladistic analyses three different approaches were used: the first was to treat the allele as a binary character; this was investigated using a Wagner parsimony algorithm. Another approach used was to consider the locus as an unordered character, using the alleles as states. Finally, we used the locus as an ordered multistate character, where mutation, fixation and elimination of each allele were treated as evolutionary novelties, and the heterozygotes were used as cues for the construction of transformation series. The trees produced by the phenetic and cladistic methods were highly congruent. This result suggests that allozymes can be used to produce phylogenetic hypotheses at higher taxonomic levels than those at which they are more usually employed. The Solé difference between the various trees was the relative positions of Bunodosoma caissarum and Bunodactis verrucosa in relation to the two species of Urticina. This difference was probably due to a high rate of anagenic change in B. verrucosa, which distorted the UPGMA dendrogram. The genera Actinia and Urticina appeared monophyletic in all of the trees produced. Also, the sea anemones with specialized column structures such as verrucae and vesicles (U.felina, U. eques, B. verrucosa, B. caissarum) formed a monophyletic cluster, a result compatible with the suggestion that these structures may have appeared only once in the evolutionary history of the Actiniidae.     

A PHYLOGENETIC ANALYSIS OF DIOON (ZAMIACEAE)

A phylogenetic analysis of all the intrageneric taxa of the genus Dioon Lindley (Zamiaceae) was undertaken by using chloroplast DNA restriction fragment length polymorphism analysis. Wagner parsimony analysis on a 187 character matrix yielded two equally parsimonious trees, differing only for the position of D. caputoi. The consensus tree has two well-defined major clades. The first is composed of D. mejiae, D. rzedowskii, and D. spinulosum; the second is composed of D. califanoi, D. caputoi, D. edule var. angustifolium, D. edule var. edule, D. holmgrenii, D. merolae, D. purpusii, D. tomasellii var. sonorense, and D. tomasellii var. tomasellii. A phenetic analysis of the same data showed results broadly congruent with the cladistic analysis. This resulting phylogeny is partially congruent with morphological data and is also compatible with the biogeography of the genus. Modem species of Dioon may have evolved as a consequence of a very fast succession of vicariance events that mainly occurred during the early Cenozoic. The short time between each of these events may not have allowed the accumulation of a large number of morphological synapomorphies for the groups of species.     

MOLECULAR GENETIC-DISTANCE ESTIMATES AMONG THE URSIDAE AS INDICATED BY ONE- AND TWO-DIMENSIONAL PROTEIN ELECTROPHORESIS

Evolutionary relationships among eight species of Ursidae (including the giant panda) relative to two Procyonidae species (raccoon and red panda) were estimated based on the extent of electrophoretic variation of 289 radiolabelled fibroblast proteins resolved by two-dimensional gel electrophoresis and among 44 isozyme loci resolved by one-dimensional electrophoresis. Allelic differences among these species were converted to genetic distances, and phenetic trees were constructed. In addition, the electrophoretic data were coded as unit characters, and minimum-length trees were derived based on the Wagner method using maximum parsimony. Regardless of the tree-building method employed, the data sets agreed on the following branching sequence: between 22.4 and 32.3 million years (MY) ago, the ancestors of the procyonids and the ursids split into two lineages. Within 10 MY, the red panda split from the line that led to the raccoon. An ancestor of the giant panda split from the ursid line 18–22 MY ago, and the South American spectacled bear split from the line leading to ursine bears 10.5–15.0 MY B.P. A group of six closely related ursine bears (brown bear, polar bear, Asiatic black bear, Malayan sun bear, American black bear, and sloth bear) diverged from a common ancestor during the past 4–8 MY. Much of this ursine radiation was not resolved by our results, with the exception of a recent (2–3 MY B.P.) divergence of brown bear and polar bear. The topological concordance of the data sets from one- and two-dimensional electrophoresis supports the usefulness of these procedures for evolutionary inference and provides additional precision to the reconstruction of divergence nodes of this carnivore group.     

Differentiation in phenotypic plasticity among populations of Arabis serrata Fr. & Sav. (Brassicaceae)

Studies on divergence of phenotypic plasticity in closely related species have suggested that character means and plasticity of these characters may evolve independently. Similar patterns of divergence between populations within a species have been reported although few plant species have been studied. Thus, in this paper, the patterns of differentiation between character means and phenotypic plasticity among eight populations of Arabis serrata are documented. Mean response and magnitude and pattern of phenotypic plasticity were measured and compared in plants growing under an environmental gradient of nutrients. Differences in means and coefficients of variation (CV as indicators of plasticity) among populations were compared using the Canberra metric and generating unrooted Wagner trees. Populations showed significant differences in character means in nine morphological traits. Magnitude and patterns of phenotypic plasticity showed a complex pattern of differentiation for each trait and population. Biomass traits were more plastic, in general, than characters associated with linear size. Comparisons between pairs of populations for nine morphological traits showed that in 28.6% of 252 possible cases, populations differed in means, magnitude and patterns of phenotypic plasticity. In almost 90% of the cases, populations differed in magnitude and/or pattern of plasticity. Considering all characters together, populations from similar habitats and with common life history features tended to respond in similar ways. The patterns of divergence, however, suggest that character means and character plasticities among populations are able to evolve independently.     

The dynamics of natural selection and vicariance in the Dominican anole: patterns of within-island molecular and morphological divergence

The larger islands of the Lesser Antilles are ecologically and geologically complex and are inhabited by single, but morphologically variable, Anolis species. Although earlier work has indicated that a large part of the morphological variation in Anolis oculatus from Dominica can be attributed to selection, a history of recurrent volcanic activity over the last few million years suggests that vicariance may have also played a significant role. We report a study of variation in the cytochrome b gene of mitochondrial DNA across the island to address this issue. We uncovered a very high degree of polymorphism, with an overall gene diversity of 0.97 and a nucleotide diversity of 0.04. Sequences, on average, differ by 3.82% and the maximum pairwise divergence (corrected for multiple hits) is 9.29%. Most haplotypes are restricted to single localities (a pattern not changed by increasing the sample size). Phylogenetic analysis revealed the presence of two distinct lineages on the island with strong phylogeographic structure. One of these is geographically restricted to a relatively small part of the central Caribbean coast. Sublineages were also discernible within the other more widely distributed lineage, but resolution within and support for these sublineages was poor. The phylogeographic pattern is not congruent with generalized body shape and scalation, but is significantly correlated with color pattern. Even when correcting for this lineage effect with partial Matrix correspondence tests, the relationship between color pattern and vegetation is reaffirmed, suggesting that although both vicariance and selection have played a role in the morphological differentiation of this species, selection for current environmental conditions has been more important. We discuss the causes of the phylogeographic structure in light of the volcanic history of the island and highlight the exceptional instance of congruence between all morphological character systems and lineage boundaries, which occurs at the transition between the northern and southern Caribbean ecotypes.     

Testing multivariate patterns of within-island differentiation in Podarcis dugesii from Madeira

Podarcis dugesii is a polymorphic species found on the ecologically-heterogeneous Atlantic island of Madeira. Patterns of geographic variation in size-free body dimensions (body shape), scalation, and size were portrayed on maps with isophene contours. There was no dominant pattern of among-site variation as seen in several other island lizards, although some linear combinations of morphological variables showed evidence of clines towards the east coast. Multivariate statistical techniques were developed to evaluate whether morphological variation contained an ecology-related spatial pattern, after removal of the effects of statistical non-independence of studied populations. Specifically, a partial correlation matrix comparison method provided evidence to support a proposed elevation model of among-site divergence in scalation and body size, with both an alternative rainfall model and spatial non-independence held constant. Similar divergence in scalation has been observed in other lizard species on other island archipelagos as well on some continental areas. The rainfall model was rejected for both body shape and scalation. The degree of within-population polymorphism in body shape and scalation showed no clear geographic trends in general, although the elevation and rainfall models could not be rejected for female scalation.     

Detecting morphological convergence in true fungi, using 18S rRNA gene sequence data.

For the true fungi, phylogenetic relationships inferred from 18S ribosomal DNA sequence data agree with morphology when (1) the fungi exhibit diagnostic morphological characters, (2) the sequence-based phylogenetic groups are statistically supported, and (3) the ribosomal DNA evolves at roughly the same rate in the lineages being compared. 18S ribosomal RNA gene sequence data and biochemical data provide a congruent definition of true fungi. Sequence data support the traditional fungal subdivisions Ascomycotina and Basidiomycotina. In conflict with morphology, some zygomycetes group with chytrid water molds rather than with other terrestrial fungi, possibly owing to unequal rates of nucleotide substitutions among zygomycete lineages. Within the ascomycetes, the taxonomic consequence of simple or reduced morphology has been a proliferation of mutually incongruent classification systems. Sequence data provide plausible resolution of relationships for some cases where reduced morphology has created confusion. For example, phylogenetic trees from rDNA indicate that those morphologically simple ascomycetes classified as yeasts are polyphyletic and that forcible spore discharge was lost convergently from three lineages of ascomycetes producing flask-like fruiting bodies.     

Comparisons of phylogenetic hypotheses among different data sets in dwarf dandelions (Krigia,Asteraceae): Additional information from internal transcribed spacer sequences of nuclear ribosomal DNA

The internal transcribed spacer (ITS) region of the 18 S–25 S nuclear ribosomal DNA repeat was sequenced from 19 populations of the tribeLactuceae, including all species of dwarf dandelion (Krigia) and five outgroup genera. The incidence of length changes and base substitutions was at least two times higher for ITS 1 than ITS 2. Interspecific sequence divergence withinKrigia averaged 9.62% (1.61%–15.19%) and 4.26% (0%–6.64%) in ITS 1 and ITS 2, respectively. Intergeneric sequence divergence ranged from 15.6% to 44.5% in ITS 1 and from 8.0% to 28.6% in ITS 2. High sequence divergence and homoplasy among genera of tribeLactuceae suggest that the phylogenetic utility of ITS sequence data is limited to interspecific studies or comparisons among closely related genera. Trees generated from ITS sequences are essentially identical to those from restriction site comparisons of the entire nuclear ribosomal (nr) DNA region. The degree of tree resolution differed depending on how gaps were treated in phylogenetic analyses. The ITS trees were congruent with the chloroplast DNA and morphological phylogenies in three major ways: 1) the sister group relationship betweenKrigia andPyrrhopappus; 2) the recognition of two monophyletic sections,Krigia andCymbia, in genusKrigia; and 3) the monophyly of theK. occidentalis-K. cespitosa clade in sect.Cymbia. However, the two nrDNA-based trees are not congruent with morphology/chloroplast DNA-based trees for the interspecific relationships in sect.Krigia. An average of 22.5% incongruence was observed among fourKrigia data sets. The relatively high degree of incongruence among data sets is due primarily to conflict between trees based on nrDNA and morphological/cpDNA data. The incongruence is probably due to the concerted evolution of nrDNA repeating units. The results fromKrigia and theLactuceae suggest that nrDNA data may have limited utility in phylogenetic studies of plants, especially in groups which exhibit high levels of sequence divergence. Our combined phylogenetic analysis as a total evidence shows the least conflict to each of the individual data sets.     

Lineages,splits and divergence challenge whether the terms anagenesis and cladogenesis are necessary

Using the framework of evolutionary lineages to separate the process of evolution and classification of species, we observe that ‘anagenesis’ and ‘cladogenesis’ are unnecessary terms. The terms have changed significantly in meaning over time, and current usage is inconsistent and vague across many different disciplines. The most popular definition of cladogenesis is the splitting of evolutionary lineages (cessation of gene flow), whereas anagenesis is evolutionary change between splits. Cladogenesis (and lineage‐splitting) is also regularly made synonymous with speciation. This definition is misleading as lineage‐splitting is prolific during evolution and because palaeontological studies provide no direct estimate of gene flow. The terms also fail to incorporate speciation without being arbitrary or relative, and the focus upon lineage‐splitting ignores the importance of divergence, hybridization, extinction and informative value (i.e. what is helpful to describe as a taxon) for species classification. We conclude and demonstrate that evolution and species diversity can be considered with greater clarity using simpler, more transparent terms than anagenesis and cladogenesis. Describing evolution and taxonomic classification can be straightforward, and there is no need to ‘make words mean so many different things’.     

A cladistic analysis of chloroplast DNA restriction site variation and morphology for the genera of the Juglandaceae

The phylogenetic relationships of the genera of the Juglandaceae are examined with cladistic analyses of chloroplast DNA (cpDNA) restriction site variation and morphology. Rates of evolution of the chloroplast genome are slower than in many other groups of plants, enabling the entire genome to be utilized at the intergeneric level. The trees resulting from the two independent analyses were completely congruent. The combined analysis of the two data sets produced a tree completely congruent with the cladogram from the two data sets analyzed independently. The cladogram is compared with previous classifications, cladistic analyses, and fossil history for the family. Although the topology resulting from the cladistic analyses of this study was strongly congruent with previous estimates of relationships within the family, the fossil record indicates that the basal-most lineages in the cladistic trees arose later than the more terminal lineages. This reversed order of origin indicates that perhaps the rooting of the trees is erroneous.     

An empirical comparison of character‐based and coalescent‐based approaches to species delimitation in a young avian complex

The process of discovering species is a fundamental responsibility of systematics. Recently, there has been a growing interest in coalescent‐based methods of species delimitation aimed at objectively identifying species early in the divergence process. However, few empirical studies have compared these new methods with character‐based approaches for discovering species. In this study, we applied both a character‐based and a coalescent‐based approaches to delimit species in a closely related avian complex, the light‐vented/Taiwan bulbul (Pycnonotus sinensis/Pycnonotus taivanus). Population aggregation analyses of plumage, mitochondrial and 13 nuclear intron character data sets produced conflicting species hypotheses with plumage data suggesting three species, mitochondrial data suggesting two species, and nuclear intron data suggesting one species. Such conflict is expected among recently diverged species, and by integrating all sources of data, we delimited three species verified with independently congruent character evidence as well as a more weakly supported fourth species identified by a single character. Attempts to validate species hypothesis using Bayesian Phylogenetics and Phylogeography (BPP), a coalescent‐based method of species delimitation, revealed several issues that can seemingly affect statistical support for species recognition. We found that θ priors had a dramatic impact on speciation probabilities, with lower values consistently favouring splitting and higher values consistently favouring lumping. More resolved guide trees also resulted in overall higher speciation probabilities. Finally, we found suggestive evidence that BPP is sensitive to the divergent effects of nonrandom mating caused by intraspecific processes such as isolation‐with‐distance, and therefore, BPP may not be a conservative method for delimiting independently evolving population lineages. Based on these concerns, we questioned the reliability of BPP results and based our conclusions about species limits exclusively on character data.     

A NUMERICAL–TAXONOMIC STUDY OF THE GENUS BULNESIA (ZYGOPHYLLACEAE): CLUSTER ANALYSIS,ORDINATION AND SIMULATION OF EVOLUTIONARY TREES

Cluster analysis by four methods, ordination by principal component analysis (PCA) and simulation of evolutionary trees (Wagner Trees) were performed on morphological data from 43 characters of eight species of the South American genus Bulnesia (Zygophyllaceae). The results of cluster analysis and principal component analysis in general agree and show that there are three pairs of taxa that appear, or obviously are, closely related. These are the pairs B. arborea–B. carrapo, B. foliosa–B. schickendantzii and B. retama–B. chilensis. These methods also indicate that the southern species B. bonariensis occupies an intermediate position between the pair of northern tropical species (B. arborea, B. carrapo) and the remaining southern species. From the beginning it was assumed that these three multifoliolate species with large flowers may be rather primitive. The Prim network indicates that these three species are closely related among themselves. Also in two of the three Wagner Trees they are placed in a group. In all cases B. sarmientoi is shown as the more remote and isolated of all species. It is regarded as a unique, specialized arboreal species showing extreme reduction in number of leaflets and carpels, leaf and flower size, etc. All graphic representations (Fig. 1–3) show the phenetic similarity or the close phylogenetic relationships of the pairs B. foliosa–B. schickendantzii and B. retama–B. chilensis to each other. These four species would represent a rather advanced group. The most xerophytic species B. retama and B. chilensis are regarded as the most advanced taxa and the most specialized histophysiologically. These occupy extreme and distant positions in PCA diagrams and Prim network, and top positions in the Wagner Trees.     

Phenetic analysis of the Mexican midland pinyon pines, Pinus cembroides and Pinus johannis

This account presents an analysis of allopatric, sympatric and juxtaposed populations of the pinyon pines, Pinus cembroides Zucc. and P. johannis M.-F. Robert, based on phenetic analysis of morphological data, and draws on a comparison and differentiation of P. culminicola Andresen & Beaman. A qualitative and quantitative database for populations has been assembled and used for a cluster and ordination analysis using NTSYS. It was found that individual populations of the taxa were distinguishable. The emergence of morphological intermediate populations between P. cembroides and P. johannis was confirmed. The pattern of variation in P. johannis was found to be discrete, showing three geographical groups. The phenetic similarity between P. johannis from Zacatecas and P. johannis from San Luis Potosi and Queretaro was lower than that of P. johannis from Zacatecas and P. culminicola from Nuevo Leon. The following traits distinguish P. cembroides and the other two species: colour and fertility of seeds; cone shape; colour and width of needles; physiognomy; seed dimensions. This last trait can be used to distinguish three subgroups of pines with white endosperm in the northern, central and southern regions of the Mexican highlands.     

Infrageneric relationships within Pogostemon Desf. (Labiatae)

Cladistic and phenetic analyses of the morphology of 79 species of Pogostemon Desf. sens lato have been undertaken. The cladistic analysis included 135 character state differences encoded as 41 binary or multistate characters. The phenetic analysis included 52 metric variables and 54 binary variables. There is a very good correspondence between the results of cladistic and phenetic analyses based on different data sets. The existence of several clearly marked clades/clusters has been demonstrated. Some groups/clades are similar to those previously taxonomically recognized but the relationships and membership of infra-generic groups have been clarified by these analyses, validating a revised infra-generic classification which has been proposed.