Society of Systematic Biologists

Annals of the Missouri Botanical Garden, Vol. 85, No. 4. (1998)

Recent cladistic analyses are revealing the phylogeny of flowering plants in increasing detail, and there is support for the monophyly of many major groups above the family level. With many elements of the major branching sequence of phylogeny established, a revised suprafamilial classification of flowering plants becomes both feasible and desirable. Here we present a classification of 462 flowering plant families in 40 putatively monophyletic orders and a small number of monophyletic, informal higher groups. The latter are the monocots, commelinoids, eudicots, core eudicots, rosids including eurosids I and II, and asterids including euasterids I and II. Under these informal groups there are also listed a number of families without assignment to order. At the end of the system is an additional list of families of uncertain position for which no firm data exist regarding placement anywhere within the system.
The Angiosperm Phylogeny Group

PLoS Comput Biol, Vol. 6, No. 8. (5 August 2010), e1000868.

The availability of genomes of many closely related bacteria with diverse metabolic capabilities offers the possibility of tracing metabolic evolution on a phylogeny relating the genomes to understand the evolutionary processes and constraints that affect the evolution of metabolic networks. Using simple (independent loss/gain of reactions) or complex (incorporating dependencies among reactions) stochastic models of metabolic evolution, it is possible to study how metabolic networks evolve over time. Here, we describe a model that takes the reaction neighborhood into account when modeling metabolic evolution. The model also allows estimation of the strength of the neighborhood effect during the course of evolution. We present Gibbs samplers for sampling networks at the internal node of a phylogeny and for estimating the parameters of evolution over a phylogeny without exploring the whole search space by iteratively sampling from the conditional distributions of the internal networks and parameters. The samplers are used to estimate the parameters of evolution of metabolic networks of bacteria in the genus Pseudomonas and to infer the metabolic networks of the ancestral pseudomonads. The results suggest that pathway maps that are conserved across the Pseudomonas phylogeny have a stronger neighborhood structure than those which have a variable distribution of reactions across the phylogeny, and that some Pseudomonas lineages are going through genome reduction resulting in the loss of a number of reactions from their metabolic networks.
Aziz Mithani, Gail Preston, Jotun Hein

SIAM J. Comput., Vol. 23, No. 6. (1994), pp. 1216-1224.

This paper presents a polynomial-time algorithm for determining whether a set of species, described by the characters they exhibit, has a perfect phylogeny, assuming the maximum number of possible states for a character is fixed. This solves a longstanding open problem. This result should be contrasted with the proof by Steel [ J. Classification , 9(1992), pp. 91--116] and Bodlaender, Fellows, and Warnow [ Proceedings of the 19 th International Colloquium on Automata, Languages, and Programming , Lecture Notes in Computer Science, 1992, pp. 273--283] that the perfect phylogeny problem is NP complete in general.
Richa Agarwala, David Baca

Mol Biol Evol, Vol. 17, No. 1. (1 January 2000), pp. 23-31.

Microsporidia are obligate intracellular parasites that were thought to be an ancient eukaryotic lineage based on molecular phylogenies using ribosomal RNA and translation elongation factors. However, this ancient origin of microsporidia has been contested recently, as several other molecular phylogenies suggest that microsporidia are closely related to fungi. Most of the protein trees that place microsporidia with fungi are not well sampled, however, and it is impossible to resolve whether microsporidia evolved from a fungus or from a protistan relative of fungi. We have sequenced beta-tubulins from 3 microsporidia, 4 chytrid fungi, and 12 zygomycete fungi, expanding the representation of beta-tubulin to include all four fungal divisions and a wide diversity of microsporidia. In phylogenetic trees including these new sequences, the overall topology of the fungal beta-tubulins generally matched the expected relationships among the four fungal divisions, although the zygomycetes were polyphyletic in some analyses. The microsporidia consistently fell within this fungal diversification, and not as a sister group to fungi. Overall, beta-tubulin phylogeny suggests that microsporidia evolved from a fungus sometime after the divergence of chytrids. We also found that chytrid alpha- and beta-tubulins are much less divergent than are tubulins from other fungi or microsporidia. In trees in which the only fungal representatives were the chytrids, microsporidia still branched with fungi (i.e., with chytrids), suggesting that the affiliation between microsporidian and fungal tubulins is not an artifact of long-branch attraction.
Patrick Keeling, Melissa Luker, Jeffrey Palmer

European Journal of Protistology, Vol. 43, No. 3. (21 August 2007), pp. 171-177.

Macroevolutionary relations among main lineages of Foraminifera have traditionally been inferred from the small subunit ribosomal genes (SSU rDNA). However, important discrepancies in the rates of SSU rDNA evolution between major lineages led to difficulties in accurate interpretation of SSU-based phylogenetic reconstructions. Recently, actin and β -tubulin sequences have been used as alternative markers of foraminiferal phylogeny and their analyses globally confirm results obtained with SSU rDNA. In order to test new protein markers, we sequenced a fragment of the largest subunit of the RNA polymerase II (RPB1), a nuclear encoded single copy gene, for 8 foraminiferal species representing major orders of Foraminifera. Analyses of our data robustly confirm previous SSU rDNA and actin phylogenies and show (i) the paraphyly and ancestral position of monothalamid Foraminifera; (ii) the independent origin of miliolids; (iii) the monophyly of rotaliids, including buliminids and globigerinids; and (iv) the polyphyly of planktonic families Globigerinidae and Candeinidae. Additionally, the RPB1 phylogeny suggests Allogromiidae as the most ancestral foraminiferal lineage. In the light of our study, RPB1 appears as a valuable phylogenetic marker, particularly useful for groups of protists showing extreme variations of evolutionary rates in ribosomal genes.
D Longet, J Pawlowski

J. Mollus. Stud., Vol. 63, No. 3. (1 August 1997), pp. 327-351.

The origin and evolution of the gastropod order Neogastropoda was investigated using an iterative, two gene (18S rDNA and cytochrome c oxidase I) approach to phylogeny reconstruction. Partial sequences spanning approximately 450 base pairs near the 5' end of the 18S rDNA gene confirmed the monophyly of Apogastropoda and its two subclades, the Caenogastropoda (including Neogastropoda and Architaenioglossa) and the Heterobranchia, but were incapable of resolving relationships among neogastropod families, or between Neogastropoda and higher Caenogastropoda. The monophyly of Heterobranchia is additionally supported by the presence within this group of a large insert of variable length in the 18S rDNA gene in the region corresponding to the E-10-1 helix of the RNA molecule. Cytochrome c oxidase I sequences were able to resolve fully the relationships among representatives of ten families of Neogastropoda. Maximum parsimony, maximum likelihood and neighbor-joining analyses of these data all revealed that Buccinoidea and Muricoidea [sensu Thiele, 1929] each represent a clade, while the families assigned by Thiele and some subsequent authors to the superfamily Volutoidea comprise a grade. Although the two toxoglossan taxa included in our study emerged as a grade rather than a clade, denser taxonomic sampling of this group will be undertaken to investigate further the paraphyly of Conoidea. Based on percent transversions at third codon positions of the CO I gene, differences among neogastropod families as well as those between the neogastropod families and Cerithium are comparable to genetic differences between orders of mammals, but are only slightly greater than differences between genera of penaeid shrimp. 10.1093/mollus/63.3.327
MG Harasewych, Laura Adamkewicz, Judith Blake, Deborah Saudek, Tracy Spriggs, Carol Bult

Zoologica Scripta, Vol. 38, No. 3. (May 2009), pp. 225-236.

Gelang, M. Cibois, A., Pasquet, E., Olsson, U., Alström, P. & Ericson, P. G. P. (2009) Phylogeny of babblers (Aves, Passeriformes): major lineages, family limits and classification. —Zoologica Scripta, 38, 225-236. Babblers, family Timaliidae, have long been subject to debate on systematic position, family limits and internal taxonomy. In this study, we use five molecular regions to estimate the relationships among a large proportion of genera traditionally placed in Timaliidae. We find good support for five main clades within this radiation, and propose a new classification, dividing the babblers into the families Sylviidae and Timaliidae. Within the latter family, four subfamilies are recognized: Zosteropinae, Timaliinae, Pellorneinae and Leiothrichinae. Several taxa, previously not studied with molecular data, are phylogenetically placed within Sylviidae or Timaliidae. This is, however, not the case for the genus Pnoepyga, for which we propose the family name Pnoepygidae fam. n.
Magnus Gelang, Alice Cibois, Eric Pasquet, Urban Olsson, Per Alstrom, PerG Ericson

Molecular phylogenetics and evolution, Vol. 23, No. 3. (June 2002), pp. 339-356.

To study the phylogenetic relationships among Anseriformes, sequences for the complete mitochondrial control region (CR) were determined from 45 waterfowl representing 24 genera, i.e., half of the existing genera. To confirm the results based on CR analysis we also analyzed representative species based on two mitochondrial protein-coding genes, cytochrome b (cytb) and NADH dehydrogenase subunit 2 (ND2). These data allowed us to construct a robust phylogeny of the Anseriformes and to compare it with existing phylogenies based on morphological or molecular data. Chauna and Dendrocygna were identified as early offshoots of the Anseriformes. All the remaining taxa fell into two clades that correspond to the two subfamilies Anatinae and Anserinae. Within Anserinae Branta and Anser cluster together, whereas Coscoroba, Cygnus, and Cereopsis form a relatively weak clade with Cygnus diverging first. Five clades are clearly recognizable among Anatinae: (i) the Anatini with Anas and Lophonetta; (ii) the Aythyini with Aythya and Netta; (iii) the Cairinini with Cairina and Aix; (iv) the Mergini with Mergus, Bucephala, Melanitta, Callonetta, Somateria, and Clangula, and (v) the Tadornini with Tadorna, Chloephaga, and Alopochen. The Tadornini diverged early on from the Anatinae; then the Mergini and a large group that comprises the Anatini, Aythyini, Cairinini, and two isolated genera, Chenonetta and Marmaronetta, diverged. The phylogeny obtained with the control region appears more robust than the one obtained with mitochondrial protein-coding genes such as ND2 and cytb. This suggests that the CR is a powerful tool for bird phylogeny, not only at a small scale (i.e., relationships between species) but also at the family level. Whereas morphological analysis effectively resolved the split between Anatinae and Anserinae and the existence of some of the clades, the precise composition of the clades are different when morphological and molecular data are compared.
Carole Donne-Goussé, Vincent Laudet, Catherine Hänni

Cladistics, Vol. 20, No. 1. (2004), pp. 64-75.

Measures of stratigraphic fit to phylogeny are analyzed to test how they are affected by the shape and size of the phylogenetic trees and by the number of stratigraphic intervals encompassed. Monte Carlo randomizations are used to investigate the sensitivity of three commonly used measures (SCI, GER and MSM*) approximating their distribution of possible values under certain conditions. All are shown to vary in different ways as parameters are varied, although MSM* seems to be the most invariant in the analyzed parameter space. These results suggest that the raw metrics should not be used for comparing the fit of different taxonomic groups or competing phylogenetic trees of the same group that differ in tree size or balance. Tree balance also affects the distributions used in significance tests based on randomization and therefore their results should not be interpreted in terms of the amount of conflict implied by a phylogenetic tree.
Diego Pol, Mark Norell, Mark Siddall

Naturwissenschaften, Vol. 95, No. 6. (1 June 2008), pp. 469-481.

Abstract  The analysis of the ever-increasing amount of biological and biomedical data can be pushed forward by comparing the data within and among species. For example, an integrative analysis of data from the genome sequencing projects for various species traces the evolution of the genomes and identifies conserved and innovative parts. Here, I review the foundations and advantages of this “historical” approach and evaluate recent attempts at automating such analyses. Biological data is comparable if a common origin exists (homology), as is the case for members of a gene family originating via duplication of an ancestral gene. If the family has relatives in other species, we can assume that the ancestral gene was present in the ancestral species from which all the other species evolved. In particular, describing the relationships among the duplicated biological sequences found in the various species is often possible by a phylogeny, which is more informative than homology statements. Detecting and elaborating on common origins may answer how certain biological sequences developed, and predict what sequences are in a particular species and what their function is. Such knowledge transfer from sequences in one species to the homologous sequences of the other is based on the principle of ‘my closest relative looks and behaves like I do’, often referred to as ‘guilt by association’. To enable knowledge transfer on a large scale, several automated ‘phylogenomics pipelines’ have been developed in recent years, and seven of these will be described and compared. Overall, the examples in this review demonstrate that homology and phylogeny analyses, done on a large (and automated) scale, can give insights into function in biology and biomedicine.
Georg Fuellen