Refuting phylogenetic relationships

Background  

Phylogenetic methods are philosophically grounded, and so can be philosophically biased in ways that limit explanatory power. This constitutes an important methodologic dimension not often taken into account. Here we address this dimension in the context of concatenation approaches to phylogeny.     

Ultrastructure and phylogenetic relationships of the unicellular green algae Ignatius tetrasporus and Pseudocharacium americanum (Chlorophyta)

The phylogenetic relationships of two unicellular green algae, Ignatius tetrasporus Bold et MacEntee and Pseudocharacium americanum Lee et Bold were investigated by ultrastructural and molecular methods. The zoospores from both species were covered neither by scales nor cell walls. The flagellar apparatus of the zoospores commonly included these features: the upper basal bodies were displaced counterclockwise in half to two‐thirds of the basal body diameter and did not overlap with each other; the lower basal bodies were directly opposed or slightly displaced clockwise; the distal fiber had gently sigmoid central striations; terminal caps were absent from the ends of the basal bodies; a V‐shaped proximal sheath extended from the upper basal bodies; a posterior fiber lay between the opposite lower basal bodies; and the coarsely striated band linked the sinister rootlet to the lower basal body. The suite of these features was not identical to that of any other quadriflagellate swimming cells, but some features including the lower basal body orientation, the striated distal fiber, and the coarsely striated fiber resemble those of the several organisms of the Siphonocladales sensu Floyd and O’Kelly. Phylogenetic analysis using 18S rDNA sequence data revealed that I. tetrasporus and P. americanum formed a monophyletic clade within the clade of Ulvophyceae sensu López‐Bautista and Chapman, but was not nested within any of the orders of the class that were examined.     

Ancient phylogenetic relationships

Traditional views on deep evolutionary events have been seriously challenged over the last few years, following the identification of major pitfalls affecting molecular phylogeny reconstruction. Here we describe the principally encountered artifacts, notably long branch attraction, and their causes (i.e., difference in evolutionary rates, mutational saturation, compositional biases). Additional difficulties due to phenomena of biological nature (i.e., lateral gene transfer, recombination, hidden paralogy) are also discussed. Moreover, contrary to common beliefs, we show that the use of rare genomic events can also be misleading and should be treated with the same caution as standard molecular phylogeny. The universal tree of life, as described in most textbooks, is partly affected by tree reconstruction artifacts, e.g. (i) the bacterial rooting of the universal tree of life; (ii) the early emergence of amitochondriate lineages in eukaryotic phylogenies; and (iii) the position of hyperthermophilic taxa in bacterial phylogenies. We present an alternative view of this tree, based on recent evidence obtained from reanalyses of ancient data sets and from novel analyses of large combination of genes.     

Reconstruction of phylogenetic relationships

In this paper, we provide an introductory overview to the field of phylogenetic analysis, which has wide applications in modern biology.     

Morphology, fossils, divergence timing, and the phylogenetic relationships of Gavialis

Although morphological data have historically favored a basal position for the Indian gharial (Gavialis gangeticus) within Crocodylia and a Mesozoic divergence between Gavialis and all other crocodylians, several recent molecular data sets have argued for a sister-group relationship between Gavialis and the Indonesian false gharial (Tomistoma schlegelii) and a divergence between them no earlier than the Late Tertiary. Fossils were added to a matrix of 164 discrete morphological characters and subjected to parsimony analysis. When morphology was analyzed alone, Gavialis was the sister taxon of all other extant crocodylians whether or not fossil ingroup taxa were included, and a sister-group relationship between Gavialis and Tomistoma was significantly less parsimonious. In combination with published sequence and restriction site fragment data, Gavialis was the sister taxon of all other living crocodylians, but the position of Tomistoma depended on the inclusion of fossil ingroup taxa; with or without fossils, preferred morphological and molecular topologies were not significantly different. Fossils closer to Gavialis than to Tomistoma can be recognized in the Late Cretaceous, and fossil relatives of Tomistoma are known from the basal Eocene, strongly indicating a divergence long before the Late Tertiary. Comparison of minimum divergence time from the fossil record with different measures of molecular distance indicates evolutionary rate heterogeneity within Crocodylia. Fossils strongly contradict a post-Oligocene divergence between Gavialis and any other living crocodylian, but the phylogenetic placement of Gavialis is best viewed as unresolved.     

Flavonoid chemistry,chromosome number and phylogenetic relationships of Helenium chihuahuensis

Five populations of Helenium chihuahuensis were examined for flavonoid content, chromosome number and morphological characteristics. Thirteen flavonoid compounds were detected of which eleven were at least partially identified and were found to be flavones. The chromosome number was determined to be $\text{2}\text{n}\text{= 15II}$. Helenium arizonicum also was found to have a chromosome number of $\text{2}\text{n}\text{= 15II}$. Helenium chihuahuensis, H. arizonicum, H. mexicanum and H. laciniatum were compared by constructing Wagner Networks, both excluding and including flavonoid data, in order to clarify their phylogenetic relationships.     

The merging of community ecology and phylogenetic biology

The increasing availability of phylogenetic data, computing power and informatics tools has facilitated a rapid expansion of studies that apply phylogenetic data and methods to community ecology. Several key areas are reviewed in which phylogenetic information helps to resolve long-standing controversies in community ecology, challenges previous assumptions, and opens new areas of investigation. In particular, studies in phylogenetic community ecology have helped to reveal the multitude of processes driving community assembly and have demonstrated the importance of evolution in the assembly process. Phylogenetic approaches have also increased understanding of the consequences of community interactions for speciation, adaptation and extinction. Finally, phylogenetic community structure and composition holds promise for predicting ecosystem processes and impacts of global change. Major challenges to advancing these areas remain. In particular, determining the extent to which ecologically relevant traits are phylogenetically conserved or convergent, and over what temporal scale, is critical to understanding the causes of community phylogenetic structure and its evolutionary and ecosystem consequences. Harnessing phylogenetic information to understand and forecast changes in diversity and dynamics of communities is a critical step in managing and restoring the Earth's biota in a time of rapid global change.     

The phylogenetic relationships of sauropod dinosaurs

A data-matrix of 205 osteological characters for 26 sauropod taxa is subjected to cladistic analysis. Two most parsimonious trees are produced, differing only in the relationships between Euhelopus, Omeisaurus and Mamenchisaurus. The monophyly of the Euhelopodidae (including Shunosaurus) is supported by seven synapomorphies. The Cetiosauridae (Patagosaurus, Cetiosaurus and Haplocanthosaurus) is paraphyletic with respect to the Neosauropoda. The latter clade divides into two major radiations–the ‘Brachiosauria’ (Camarasaurus, brachiosaurids and titanosauroids), and the Diplodocoidea (nemegtosaurids, dicraeosaurids, diplodocids and Rebbachisaurus). Further evidence for the inclusion of Opisthocoelwaudia in the Titanosauroidea is presented. Phuwiangosaurus, a problematic sauropod from Thailand, may represent one of the most plesiomorphic titanosauroids. ‘Peg’-like teeth have evolved at least twice within the Sauropoda. The postspinal lamina, on the neural spines of middle and caudal dorsal vertebrae, represents a neomorph rather than a fusion of pre-existing structures. Forked chevrons may have evolved convergently in the Euhelopodidae and the diplodocid-dicraeosaurid clade, or they may have been acquired early in sauropod evolution and subsequently lost in the ‘Brachiosauria’. The strengths and weaknesses of the data-matrix and tree topologies are explored using bootstrapping, decay analysis and randomization tests. Several nodes are only poorly supported, but this seems to reflect the large proportion of missing data in the matrix (～46%), rather than an abnormally high level of homoplasy. The results of the randomization tests indicate that the ‘data-matrix’ probably contains a strong phylogenetic ‘signal’. The relationships of some forms, such as Haplocanthosaurus, are influenced by the inclusion or exclusion of certain taxa with unusual combinations of character states. Such a result suggests that there are dangers inherent in the view that ‘higher’ level sauropod phylogeny can be accurately reconstructed using only a small number of well-known taxa.     

The phylogenetic relationships of argyrolagid marsupials

New material of the oldest known argyrolagid marsupial Proargyrolagus bolivianus from the late Oligocene of Bolivia is described. The new specimen preserves previously unknown aspects of the anterior dentition that solve the long-standing homology problem concerning the identity (i2) of the procumbent lower incisors in argyrolagids. This new anatomical information is incorporated into a morphology-based phylogenetic analysis of all extant marsupial families and Argyrolagidae, with the aim of testing the monophyly of Paucituberculata and evaluating the relationships among extant marsupial families. Eleven features support the monophyly of Paucituberculata, the following three unique among Marsupialia: small size of the paraconid, procumbent second lower incisor, and supraoccipital without distinct lambdoid crest resulting in globular form of braincase. Paucituberculata is the sister group of an Australian clade of marsupials that includes Dromiciops, but these results are not robust, as shown by sensitivity analyses. The foramen ovale surrounded completely by the alisphenoid supports the association of Dromiciops with diprotodontians.     

Beta-keratins of the crocodilian epidermis: composition, structure, and phylogenetic relationships

Nucleotide and deduced amino acid sequences of three beta-keratins of Nile crocodile scales are presented. Using 5'- and 3'-RACE analysis, two cDNA sequences of 1 kb (Cr-gptrp-1) and 1.5 kb (Cr-gptrp-2) were determined, corresponding to 17.4 and 19.3 kDa proteins, respectively, and a pI of 8.0. In genomic DNA amplifications, we determined that the 5'-UTR of Cr-gptrp-2 contains an intron of 621 nucleotides. In addition, we isolated a third gene (Cr-gptrp-3) in genomic DNA amplifications that exhibits seven amino acid differences with Cr-gptrp-2. Genomic organization of the sequenced crocodilian beta-keratin genes is similar to avian beta-keratin genes. Deduced proteins are rich in glycine, proline, serine, and tyrosine, and contain cysteines toward the N- and C-terminal regions, likely for the formation of disulfide bonds. Prediction of the secondary structure suggests that the central core box of 20 amino acids contains two beta-strands and has 75-90% identity with chick beta-keratins. Toward the C-terminus, numerous glycine-glycine-tyrosine and glycine-glycine-leucine repeats are present, which may contribute to making crocodile scales hard. In situ hybridization shows expression of beta-keratin genes in differentiating beta-cells of epidermal transitional layers. Phylogenetic analysis of the available archosaurian and lepidosaurian beta-keratins suggests that feather keratins diversified early from nonfeather keratins, deep in archosaur evolution. However, only the complete knowledge of all crocodilian beta-keratins will confirm whether feather keratins have an origin independent of those in bird scales, which preceded the split between birds and crocodiles.     

Morphology,biology, and systematic relationships ofDesmaria (Loranthaceae)

Desmaria mutabilis is unique inLoranthaceae in having dimorphic shoots, the short shoots producing a terminal inflorescence. Other unusual features in the family are well differentiated bud scales and deciduousness. The normal position of mature plants on the trunks of large trees is shown to be a consequence of profuse vegetative reproduction from the epicortical roots, the predominant growth direction of the latter towards the trunk from the original site of establishment on a lateral branch, and the ability of epicortical roots to generate haustorial contacts through heavy host bark. The seedling is heterocotylar, one cotyledon being phanerocotylar, the other cryptocotylar and functioning as a haustorial organ in the endosperm. It is suggested thatDesmaria is a member of the primitive complex of loranthaceous genera which includesGaiadendron.     

Multigene analysis of lophophorate and chaetognath phylogenetic relationships

Maximum likelihood and Bayesian inference analyses of seven concatenated fragments of nuclear-encoded housekeeping genes indicate that Lophotrochozoa is monophyletic, i.e., the lophophorate groups Bryozoa, Brachiopoda and Phoronida are more closely related to molluscs and annelids than to Deuterostomia or Ecdysozoa. Lophophorates themselves, however, form a polyphyletic assemblage. The hypotheses that they are monophyletic and more closely allied to Deuterostomia than to Protostomia can be ruled out with both the approximately unbiased test and the expected likelihood weights test. The existence of Phoronozoa, a putative clade including Brachiopoda and Phoronida, has also been rejected. According to our analyses, phoronids instead share a more recent common ancestor with bryozoans than with brachiopods. Platyhelminthes is the sister group of Lophotrochozoa. Together these two constitute Spiralia. Although Chaetognatha appears as the sister group of Priapulida within Ecdysozoa in our analyses, alternative hypothesis concerning chaetognath relationships could not be rejected.     

The phylogenetic relationships of Chalcosiinae (Lepidoptera, Zygaenoidea, Zygaenidae)

The chalcosiine zygaenid moths constitute one of the most striking groups within the lower-ditrysian Lepidoptera, with highly diverse mimetic patterns, chemical defence systems, scent organs, copulatory mechanisms, hostplant utilization and diapause biology, plus a very disjunctive biogeographical pattern. In this paper we focus on the genus-level phylogenetics of this subfamily. A cladistic study was performed using 414 morphological and biochemical characters obtained from 411 species belonging to 186 species-groups of 73 genera plus 21 outgroups. Phylogenetic analysis using maximum parsimony leads to the following conclusions: (1) neither the current concept of Zygaenidae nor that of Chalcosiinae is monophyletic; (2) the previously proposed sister-group relationship of Zygaeninae + Chalcosiinae is rejected in favour of the relationship (Zygaeninae + ((Callizygaeninae + Cleoda ) + ( Heteropan + Chalcosiinae))); (3) except for the monobasic Aglaopini, none of the tribes sensu Alberti (1954 ) is monophyletic; (4) chalcosiine synapomorphies include structures of the chemical defence system, scent organs of adults and of the apodemal system of the male genitalia. A paired metathoracic androconial organ and a series of abdominal tergal corematal organs have been discovered, both being new to Lepidoptera. Due to highly homoplastic patterns in copulatory structures and wings that demonstrate significant sexual dimorphism, polymorphism and mimicry, 17 of the 69 'true' chalcosiine genera ( c . 25%) are shown to be either paraphyletic or polyphyletic. The present classification is therefore very misleading. Reductions of various parts of the male genitalia in some groups are accompanied by morphological and functional replacement involving the 8th abdominal segment. A prominent but convergent lock and key mechanism is revealed.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 143 , 161–341.     

Species boundaries,phylogenetic relationships,and ecological differentiation inAnthriscus (Apiaceae)

Species boundaries and phylogenetic relationships of 17 taxa ofAnthriscus (Apiaceae), with special emphasis on the critical sect.Cacosciadium, were explored using morphological data with principal component analysis, phenetics, and phylogenetics. The analyses did not provide satisfactory resolution of taxa from sect.Cacosciadium and only four species were retained. The total number of species was reduced to nine. Sect.Cacosciadium is distinguished by only two synapomorphies while sects.Anthriscus andCaroides are better supported. Present geographic and ecological variation suggests that the radiation ofAnthriscus occurred through divergence of peripheral isolated populations adapting to different habitats: high montane meadows and screes, shady climax forests, and seasonally dry habitats at lower altitudes. The adaptive significance of particular morphological traits is discussed.     

Exploring contradictory phylogenetic relationships in yeasts

Phylogenetic trees underlie our understanding of yeast evolution and are also proving instrumental in the development of a more robust yeast classification system based upon natural (i.e. evolutionary) relationships. In an effort to refine/improve taxonomic resolution, recent studies have focused on the use of multigene rather than single gene sequencing. Nevertheless, searches to determine 'the tree' remain problematic, as they can often overlook conflicts in the dataset. In such instances, phylogenetic networks such as neighbor-nets and consensus networks can provide a more useful and indeed more informative alternative means of analysis. In this study, we have used the latter two phylogenetic network techniques to reanalyze the multigene sequence dataset of Kurtzman & Robnett, which was used to redefine the taxonomy of the family Saccharomycetaceae. Results from our analyses show that, in general, established clades are robust. However, they also reveal conflict between mitochondrial- and nuclear-encoded genes and indicate the existence of complex patterns of hybridization and introgression not detected in the original study. These patterns are discussed in relation to how they may impact upon the current classification of this group of yeasts.     

Modelling phylogenetic relationships using reticulated networks

Makarenkov, V., Legendre, P. & Desdevises, Y. (2004). Modelling phylogenetic relationships using reticulated networks. —  Zoologica Scripta , 33 , 89–96.
Most traditional methods of phylogenetic analysis assume that species evolution can be represented by means of a bifurcating tree model. In many phylogenetic situations, however, some of the evolutionary links between species are due to reticulate evolution. For instance, reticulate models can adequately describe such complicated mechanisms as lateral gene transfer in bacteria or species hybridization. The theoretical concepts of reticulate evolution developed in the 1980s and 1990s need to be supported by appropriate analytical tools and software. In this paper, we present the main features of a new distance-based method for modelling phylogenetic relationships among species by means of reticulated networks (RNs). The method uses the least-squares model to build a RN by gradually improving upon the solution provided by a phylogenetic tree. A computer program facilitating the reconstruction and visualization of reticulate phylogenies is made available to researchers. In the application section, we illustrate the usefulness of the method by studying the evolution of honeybees (genus Apis ). The method for reconstructing RNs has been included in the T-Rex ( Tree and Reticulogram Reconstruction ) package recently developed by the first-named author.