Evolution and character congruence in some western Indian Ocean Phelsuma: Numerical analysis of biochemistry, shape and scalation

The evolution of five island populations of Green gecko, representing inter- and intra-specific divergence, was studied using biochemical data, scalation and shape. The data were numerically analysed using ordination analyses for the phenetic classification and Wagner trees to hypothesize the phylogeny. These studies revealed three phenetic groups corresponding to three mono-phyletic lineages. The numerical analysis of morphological data agreed with the numerical analysis of biochemical data. It is concluded that the classification based on biochemical affinities differed from the previous classification based on conventional analysis of morphology due to methodological and philosophical differences rather than differences between morphological and biochemical evolution.
The ordination analyses were very congruent between data sets (biochemical, shape, scalation, total) and the Wagner trees were generally congruent between data sets. Some Wagner trees based on scalation data were incongruent. The phenetic and cladistic classifications corresponded to each other but differed from the conventional classification. The phylogenetic analysis of the total data set indicated that the three specific lineages showed relatively equal anagenesis. However, anagenic divergence differed markedly between character types. It is suggested that a range of character types be used when studying anagenesis.     

THE PHYLOGENETIC RELATIONSHIPS AMONG REQUIEM AND HAMMERHEAD SHARKS: INFERRING PHYLOGENY WHEN THOUSANDS OF EQUALLY MOST PARSIMONIOUS TREES RESULT

Abstract— Protein variation among 37 species of carcharhiniform sharks was examined at 17 presumed loci. Evolutionary trees were inferred from these data using both cladistic character and a distance Wagner analysis. Initial cladistic character analysis resulted in more than 30 000 equally parsimonious tree arrangements. Randomization tests designed to evaluate the phylogenetic information content of the data suggest the data are highly significantly different from random in spite of the large number of parsimonious trees produced. Different starting seed trees were found to influence the kind of tree topologies discovered by the heuristic branch swapping algorithm used. The trees generated during the early phases of branch swapping on a single seed tree were found to be topologically similar to those generated throughout the course of branch swapping. Successive weighting increased the frequency and the consistency with which certain clades were found during the course of branch swapping, causing the semi-strict consensus to be more resolved. Successive weighting also appeared resilient to the bias associated with the choice of initial seed tree causing analyses seeded with different trees to converge on identical final character weights and the same semi-strict consensus tree.
The summary cladistic character analysis and the distance Wagner analysis both support the monophyly of two major clades, the genus Rhizoprionodon and the genus Sphyrna. . The distance Wagner analysis also supports the monophyly of the genus Carcharhinus . However, the cladistic analysis suggests that Carcharhinus is a paraphyletic group that includes the blue shark Prionace glauca .     

中国猕猴桃属植物叶表皮毛策形态特征及数量分类分析

选取国产猕猴桃３５个分类群的代表植株,应用光学显微对其新鲜叶表皮毛的微形态特征,形体大小、细胞结构、分布和密度等多态性状和数量性状进行了观察和测量,该属植物的叶表皮毛微形态特征可归纳为６个类型：１）单细胞毛;２）单列多细胞毛,每形单列毛、泡状单列毛、扭曲毛、直壁单列毛、曲壁单列毛;３）多列渐尖毛和急尖毛,包括多列曲壁渐尖毛和急尖毛,多列直壁渐尖毛和急尖毛;４）多列粗毛,包括柱状毛,多列渐尖粗毛,多     

Quantitative taxonomic analyses of Actinidia (Actinidiaceae) in China based on micromorphological characters of foliar trichomes

There are various arguments on classification of the genus Actinidia Lindl., a genus with approximately 63 species, 59 of which have been found in China. The paper investigated the characteristics of foliar trichomes of 35 taxa from China under optical microscope, including size, celluar structure, distribution and density. According to their micromorphological characteristics, foliar trichomes can be classified into the following six categories: 1) single-cell hairs; 2) uniseriate hairs, including linear, bulbous, twisted, straight-walled, and bent-walled hairs; 3) multiseriate hairs, including twisted, straight-walled and gradually sharpening, straight-walled and suddenly sharpening, bent-walled and gradually sharpening, and suddenly sharpening hairs; 4) multiseriate thick hairs, including pillar hairs, gradually sharpening thick hairs, and suddenly sharpening thick hairs; 5) stellate hairs, including parenchyma-stellate and sclerenchyma-stellate (normal state and special states such as rosulate, peltate-stellate, and overlopping-stellate) hairs; and 6) dichotomous hairs. On the basis of the micromorphological characteristics of foliar trichomes in Actinidia, with Clematoclethra lasioclada as an outgroup, both the quantitative cladistic analysis and phenetic analysis were performed using Wagner method and UPGMA clustering method respectively to reconstruct the phylogeny of Actinidia in China. The phylogenetic tree generated by cladistic analysis suggests that the sect. Leiocarpae be a monophyletic group, but other three sections, i.e., sect. Maculatae, sect. Strigosae and sect. Stellatae, be non-monophyletic groups. The results obtained from the phenetic analysis reflect relationships among the taxa of Actinidia in China, especially a close relationship between A. chinensis and A. deliciosa, and a relatively remote relationship between A. callosa var. henryi and A. callosa var. discolor. In conclusion, the micromorphological characters of foliar trichomes and the methods of quantitative taxonomic analysis are of key importance tostudies on phylogenetic and phenetic relationships of Actinidia.     

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.     

When phylogenetics met biogeography: Willi Hennig,Lars Brundin and the roots of phylogenetic and cladistic biogeography

Willi Hennig's (Beitr. Ent. 1960, 10, 15) Die Dipteren-Fauna von Neuseeland als systematisches und tiergeographisches Problem applied a phylogenetic approach to examine the distributional patterns exhibited by the Diptera of New Zealand. Hennig showed how phylogenetic trees may be used to infer dispersal, based on the progression and deviation rules, and also discussed the existence of vicariance patterns. The most important author who applied Hennig's phylogenetic biogeography was Lars Brundin, when analysing the phylogenetic relationships of two taxa of Chironomidae (Diptera) and using them to examine the biogeographic relationships of Australia, New Zealand, South America and South Africa. The relevance of Brundin's contribution was noted by several authors, as it began the cladistic or vicariance approach to biogeography, that implies the discovery of vicariance events shared by different monophyletic groups. Both phylogenetic and cladistic biogeography have a place in contemporary biogeography, the former for analysing taxon biogeography and the latter when addressing Earth or biota biogeography. The recent use of the term “phylogenetic biogeography” to refer to a posteriori methods of cladistic biogeography is erroneous and should be avoided.     

ACCURACY OF ESTIMATED PHYLOGENIES: EFFECTS OF TREE TOPOLOGY AND EVOLUTIONARY MODEL

A simulation study was carried out to investigate the relative importance of tree topology (both balance and stemminess), evolutionary rates (constant, varying among characters, and varying among lineages), and evolutionary models in determining the accuracy with which phylogenetic trees can be estimated. The three evolutionary context models were phyletic (characters can change at each simulated time step), speciational (changes are possible only at the time of speciation into two daughter lineages), and punctuational (changes occur at the time of speciation but only in one of the daughter lineages). UPGMA clustering and maximum parsimony (“Wagner trees”) methods for estimating phylogenies were compared. All trees were based on eight recent OTUs. The three evolutionary context models were found to have the largest influence on accuracy of estimates by both methods. The next most important effect was that of the stemminess × context interaction. Maximum parsimony and UPGMA performed worst under the punctuational models. Under the phyletic model, trees with high stemminess values could be estimated more accurately and balanced trees were slightly easier to estimate than unbalanced ones. Overall, maximum parsimony yielded more accurate trees than UPGMA—but that was expected for these simulations since many more characters than OTUs were used. Our results suggest that the great majority of estimated phylogenetic trees are likely to be quite inaccurate; they underscore the inappropriateness of characterizing current phylogenetic methods as being for reconstruction rather than for estimation.     

Interspecific relationship of ten European orchid species as revealed by enzyme electrophoresis

Ten species of orchid plants belonging to the generaOrchis (7),Dactylorhiza (2), andGymnadenia (1) were analyzed by enzyme electrophoresis. Each species can be identified by a combination of enzyme bands different from those of all other species examined. The electrophoretic data were used for the construction of phenetic and phylogenetic trees with the help of computer programs. The trees were almost identical regardless which method was used. Our results differ considerably from a classification based on morphological evidence. The electrophoretic data indicate that the genusOrchis is not a monophyletic group.     

Relationships of the Insect-Pathogenic Order Entomophthorales (Zygomycota, Fungi) Based on Phylogenetic Analyses of Nuclear Small Subunit Ribosomal DNA Sequences (SSU rDNA)

We sequenced the nuclear small subunit of ribosomal DNA (SSU rDNA) from seven species within the insect-pathogenic order Entomophthorales. These sequences were aligned with other published SSU rDNA sequences and phylogenies were inferred using phenetic and cladistic methods. Based on three different phylogenetic methods the Entomophthorales (excludingBasidiobolus ranarum) is monophyletic;B. ranarumwas more closely related to chytrids from Chytridiales and Neocallimasticales than to Entomophthorales, as was proposed by Nagahamaet al.(Mycologia87:203–209, 1995). Nuclear characters (large nuclei containing conspicuous condensed chromatin and lack of a prominent nucleolus) were of predictive value for the monophyly of the family Entomophthoraceae. Conidial characters separate the Entomophthoraceae, which only includes obligate pathogens, into at least two lineages: one lineage with uninucleate conidia and another with multinucleate conidia. The two species ofConidiobolusstudied were paraphyletic in our analyses and only distantly related to each other. This information may prove to be important in the use of these fungi as biocontrol agents.     

Phylogenetic analysis of eleven species of Biomphalaria Preston, 1910 (Gastropoda: Planorbidae) based on comparisons of allozymes

Freshwater snails in the genus Biomphalaria transmit Schistosoma mansoni in Africa, South America and the Caribbean region. Although considerable attention has been given to the identification of species, little is known of evolutionary relationships among the species. A phylogenetic analysis of 25 populations representing 11 species was performed on 25 enzyme loci examined using starch gel electrophoresis. A phylogenetic analysis of the individual populations produced 60 trees of equal length. The 60 trees have a consistency index value of 75.9% and a retention index value of 76.5%. The phylogenetic analysis provided strong support for the monophyly of Biomphalaria with either 14 or 15 synapomorphies uniting all of the species included and separating them from the outgroup, two species of Helisoma. Four nominal species represented by multiple populations formed monophyletic groups. Populations of B. sudanica, B. choanomphala, and B. alexandrina were interspersed. Ten arrangements were obtained for the populations of these three species. A variety of ingroup taxa were used to root the trees, and all provided support for the use of Helisoma species as an outgroup. In all of the trees obtained, the African species together formed a monophyletic group. In none of the trees obtained did the neotropical species form a monophyletic group. A constrained analysis requiring the monophyly of the neotropical species as well as the African species resulted in 90 trees just two steps longer than the shortest trees. Analysis of the species from either hemisphere alone resulted in decreased resolution, as measured by an increase in the number of trees obtained. This finding suggests that further comparisons of species from the two hemispheres will be of considerable value. Finally, two species which are resistant to infection with S. mansoni were included among the eleven studied. Neither of these species formed the sister group to all of the other species included, indicating that susceptibility is the plesiomorphic state, and that resistance is derived. Similarly, in none of the trees obtained did the two resistant species fall out as sister taxa, indicating that resistance arose independently twice.     

Phylogeny of the sabertoothed felids (Carnivora: Felidae: Machairodontinae)

In recent years, advances in our understanding of feline relationships have cast light on their evolutionary history. In contrast, there have been no phylogenetic analyses on machairodont felids, making it difficult to develop an evolutionary hypothesis based on the recent surge of studies on their craniomandibular morphology and functional anatomy. In this paper, I provide the first phylogenetic hypothesis of machairodont relationships based on 50 craniomandibular and dental characters from a wide range of sabercats spanning more 11 Myr. Exact searches produced 19 most‐parsimonious trees, and a strict consensus was well resolved. The Machairodontinae comprise a number of basal taxa (Promegantereon, Machairodus, Nimravides, Dinofelis, Metailurus) and a well‐supported clade of primarily Plio‐Pleistocene taxa (Megantereon, Smilodon, Amphimachairodus, Homotherium, Xenosmilus) for which the name Eumachairodontia taxon novum is proposed. Previous phenetic grouping of machairodont taxa into three distinct groups, the Smilodontini, Homotherini and Metailurini, was not supported by cladistic parsimony analysis, and forcing monophyly of these groups was significantly incompatible with character distribution. Machairodonts as a clade are not characterized by saberteeth, i.e. hypertrophied, blade‐like upper canines, but by small lower canines, as well as small M¹; and large P³ parastyle. True saberteeth arose later and are a synapomorphy of the Eumachairodontia.     

Chloroplast DNA-based phylogeny of AsianPinus species (Pinaceae)

The genusPinus includes over 90 species with approximately 24 species native to Asia. We have analyzed the chloroplast (cp) DNA variation of 18Pinus species, including 15 Asian, two Eurasian, and one European species using seven restriction enzymes and ten non-overlapping probes and inferred their phylogenetic relationships. Results of phenetic and cladistic approaches to phylogeny reconstruction were largely in agreement, suggesting two major lineages within the genus and confirmed the ancient character of haploxylon and diploxylon subgenera. Species from sectionParrya appear to have diverged earliest from the hypothesized phylogenetic centre for the haploxylon pines, withP. bungeana andP. gerardiana forming two basal, monotypic lineages. The range of estimated pairwise nucleotide substitutions per site ( ) was higher among haploxylon pines than among diploxylon species. CpDNA divergence was found to be low within the sectionSylvestres, relative to the divergence among haploxylon species, suggesting that the radiation of this group of taxa from its common ancestor occurred after the diversification of other groups. The low cpDNA divergence in this subsection corroborated earlier evidence for its phylogenetic cohesiveness and existence as a monophyletic group.     

Phylogeny of New Zealand hepialid moths (Lepidoptera: Hepialidae) inferred from a cladistic analysis of morphological data

The phylogeny of the New Zealand hepialid moths was estimated from a cladistic analysis of sixty‐three morphological characters, from all life cycle stages. One hundred and sixteen maximum parsimony trees were produced. The phylogenetic reconstruction indicated that the currently recognized generic concepts, and the four informal lineages hypothesized in a previous morphological taxonomic revision, were monophyletic. The relationships of species within genus Wiseana were not fully resolved. Analysis of a data set of thirty‐nine adult male characters from the New Zealand taxa and the Australian genera Jeana, Oxycanus and Trictena supported the monophyly of the New Zealand ‘Oxycanus’ s.s lineage.     

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.     

Root causes of phylogenetic incongruence observed within basal sauropodomorph interrelationships

The relationships among basal sauropodomorphs are controversial. Results of cladistic analyses vary from a fully paraphyletic assemblage to a monophyletic core‐prosauropod. We apply the comparative cladistics method to three published cladistic analyses of sauropodomorph dinosaurs, in order to identify root causes for differences between phylogenetic results. Except for three taxa (Saturnalia, Thecodontosaurus, and Efraasia) and one clade (Gravisauria), the remaining genera are recovered with conflicting positions. The comparative method is based on indices that allow for the quantification of the degree of similarity in characters and character states among analyses. A comparison of primary data, character selection, and scoring highlights significant discrepancies in data sets. Our results suggest that one character out of two varies from one analysis to the other. These are the root causes for the phylogenetic incongruence observed. The hurdle of the phylogenetic definition of the clade Sauropoda, which has been defined in four different ways, is also treated. We concur with several recent papers following the first node‐based definition of Sauropoda. © 2015 The Linnean Society of London     

Cladistic analysis of the Cirripedia Thoracica

We present a cladistic analysis of the Cirripedia Thoracica using morphological characters and the Acrothoracica and Ascothoracida as outgroups. The list of characters comprised 32 shell and soft body features. The operational taxonomic units (OTUs) comprised 26 well-studied fossil and extant taxa, principally genera, since uncertainty about monophyly exists for most higher ranking taxonomic units. Parsimony analyses using PAUP 3.1.1 and Hennig86 produced 189 trees of assured minimal length. We also examined character evolution in the consensus trees using MacClade and Clados. The monophyly of the Balanomorpha and the Verrucomorpha sensu stricto is confirmed, and all trees featured a sister group relationship between the ‘living fossil Neoverruca and me Brachylepadomorpha. In the consensus trees the sequential progression of ‘pedunculate‘sister groups up to a node containing Neolepas also conforms to current views, but certain well-established taxa based solely on plesiomorphies stand out as paraphyletic, such as Pedunculata (= Lepadomorpha); Eolepadinae, Scalpellomorpha and Chthamaloidea. The 189 trees differed principally in the position of shell-less pedunculates, Neoverruca, the scalpelloid Capitulum, and the interrelationships within the Balanomorpha, although the 50% majority rule consensus tree almost fully resolved the latter. A monophyletic Sessilia comprising both Verrucomorpha and Balanomorpha appeared among the shortest trees, but not in the consensus. A tree with a monophyletic Verrucomorpha including Neoverruca had a tree length two steps longer than the consensus trees. Deletion of all extinct OTUs produced a radically different tree, which highlights the importance of fossils in estimating cirripede phylogeny. Mapping of our character set onto a manually constructed cladogram reflecting die most recent scenario of cirripede evolution resulted in a tree length five steps longer than any of our shortest trees. Our analysis reveals that several key questions in cirripede phylogeny remain unsolved, notably the position of shell-less forms and the transition from ‘pedunculate‘to ‘sessile‘barnacles. The inclusion of more fossil species at this point in our understanding of cirripede phylogeny will only result in even greater levels of uncertainty. When constructing the character list we also identified numerous uncertainties in the homology of traits commonly used in discussing cirripede evolution. Our study highlights larval ultrastructure, detailed studies of early ontogeny, and molecular data as the most promising areas for future research.     

An investigation into the application of the Wagner parsimony method in synecology

Synecological analyses are usually based on typological, phenetic and cladistic methods. The disadvantages of these techniques are shown. The application of the Wagner parsimony method to synecology is considered. All the methods need some prerequisites, viz. definitions of localities and characters (the most simple one being the presence/absence of taxa); the choice of taxonomic level of taxa; their autochthony. The application of Wagner parsimony needs a new terminology. The congruence of any environmental condition, including freshwater monitoring indices, can be tested on parsimonious trees. The Wagner parsimony method not only provides various indices (tree length, CI, HI, RC, RI) which allow the comparison of trees but also minimal trees which are direct tools in synecology.     

REEXAMINATION OF PHYLOGENETIC RELATIONSHIPS WITHIN THE COLONIAL VOLVOCALES (CHLOROPHYTA): AN ANALYSIS OF atpB AND rbcL GENE SEQUENCES

The chloroplast-encoded atp B gene was sequenced from 33 strains representing 28 species of the colonial Volvocales (the Volvocaceae and its relatives) to reexamine phylogenetic relationships as previously deduced by morphological data and rbc L gene sequence data.1128 base pairs in the coding regions of the atp B gene were analyzed by MP, NJ, and ML analyses. Although supported with relatively low bootstrap values (75% and 65% in the NJ and ML analyses, respectively), three anisogamous/oogamous volvocacean genera— Eudorina, Pleodorina, and Volvox, excluding the section Volvox (= Euvolvox, illegitimate name), constituted a large monophyletic group (Eudorina group). Outside the Eudorina group, a robust lineage composed of three species of Volvox sect. Volvox was resolved as in the rbc L gene trees, rejecting the hypothesis of the previous cladistic analysis based on morphological data that the genus Volvox is monophyletic. In addition, the NJ and ML trees suggested that Eudorina is a nonmonophyletic genus as inferred from the morphological data and rbc L gene sequences. Although phylogenetic status of the genus Gonium is ambiguous in the rbc L gene trees and the paraphyly of this genus is resolved in the cladistic analysis based on morphological data, the atp B gene sequence data suggest monophyly of Gonium with relatively low bootstrap values (56–61%) in the NJ and ML trees. On the basis of the combined sequence data (2256 base pairs) from atp B and rbc L genes, Gonium was resolved as a robust monophyletic genus in the NJ and ML trees (with 68–86% bootstrap values), and Eudorina elegans Ehrenberg represented a paraphyletic species positioned most basally within the Eudorina group. However, phylogenetic status and relationships of the families of the colonial Volvocales were still almost ambiguous even in the combined analysis.