Congruence between phylogenetic and stratigraphic data on the history of life

The quality of the fossil record and the accuracy of reconstructed phylogenies have been debated recently, and doubt has been cast on how far current knowledge actually reflects what happened in the past. A survey of 384 published cladograms of a variety of animals (echinoderms, fishes, tetrapods) shows that there is good agreement between phylogenetic (character) data and stratigraphic (age) data, based on a variety of comparative metrics. This congruence of conclusions from two essentially independent sources of data confirms that the majority of cladograms are broadly accurate and that the fossil record, incomplete as it is, gives a reasonably faithful documentation of the sequence of occurrence of organisms through time.     

Effect of genetic convergence on phylogenetic inference

Phylogenetic reconstructions are a major component of many studies in evolutionary biology, but their accuracy can be reduced under certain conditions. Recent studies showed that the convergent evolution of some phenotypes resulted from recurrent amino acid substitutions in genes belonging to distant lineages. It has been suggested that these convergent substitutions could bias phylogenetic reconstruction toward grouping convergent phenotypes together, but such an effect has never been appropriately tested. We used computer simulations to determine the effect of convergent substitutions on the accuracy of phylogenetic inference. We show that, in some realistic conditions, even a relatively small proportion of convergent codons can strongly bias phylogenetic reconstruction, especially when amino acid sequences are used as characters. The strength of this bias does not depend on the reconstruction method but varies as a function of how much divergence had occurred among the lineages prior to any episodes of convergent substitutions. While the occurrence of this bias is difficult to predict, the risk of spurious groupings is strongly decreased by considering only 3rd codon positions, which are less subject to selection, as long as saturation problems are not present. Therefore, we recommend that, whenever possible, topologies obtained with amino acid sequences and 3rd codon positions be compared to identify potential phylogenetic biases and avoid evolutionarily misleading conclusions.     

The colubrid radiation in Africa (Serpentes: Golubridae): phylogenetic relationships and evolutionary patterns based on immunological data

Phylogenetic relationships among genera of African colubrids were evaluated using estimates of divergence among serum albumins compared by microcomplement fixation. Representatives of about half of the extant genera of African colubrids, as well as the Elapidae, Atractaspis and the Madagascan colubrid Leioheterodon, were analysed. The tree of best fit to the data has an unresolved basal polychotomy comprising at least five lineages of colubrids, as well as Elapidae and Atractaspis; thus, colubrids were not demonstrably monophyletic with these data. Two cosmopolitan clades, colubrines and natricines, are represented in Africa by series of closely related genera, but divergence among other genera is relatively great. Rate tests show that this is apparently not due to higher rates of albumin evolution in these, relative to other colubrids. Among the other associations supported by the immunological data are: (1) Psammophis-(Rhamphiophis-Dipsina)-Malpolon-Psammophylax; (2) Amblyodipsas-Macrelaps; (3) (Lycodonomorphus-Lamprophis)-Mehelya; and (4) Colubrinae-Natricinae. Grayia is questionably associated with the colubrine-natricine lineage. Prosymna and Lycodon are clearly members of the colubrine clade, and Amplorhinus possibly associates with Leioheterodon. Gonionotophis, Duherria, Lycophidion and Pseudaspis show no strong association with any other genera, and represent other basal or near-basal clades within the colubrid/elapid radiation. The immunological data do not support a clade comprising the Elapidae, Atractaspis and some ‘aparallactines’ relative to Viperidae and other colubrids. The basal colubrid-elapid-Atractaspis divergence occurred more than 30 Myr ago, and the fossil record of colubrids in Africa greatly underestimates both the age and clade diversity of this group. In contrast to the pattern of radiation in the neotropics, where most colubrids belong to one of three major clades, in Africa only the colubrine lineage comprises a substantial portion of the extant generic diversity; most other genera stem from relatively ancient cladogenetic events and have few living representatives.     

Environmental implications of pollen spectra in bat droppings from southeastern Spain and potential for palaeoenvironmental reconstructions

Pollen was analysed from bat guano from nine caves in southeastern Spain and surface soils in their immediate surroundings. We compare the pollen spectra of 34 modern dung samples from the nine caves with one modern surface pollen sample from each cave. The contents suggest reasonable pollen diversity and richness, including anemophilous and zoophilous pollen types. Since the latter is usually under-represented in atmospheric pollen, the guano spectra therefore appear to reflect the vegetation more effectively than normal surface soil samples. Despite health hazards such as histoplasmosis, the difficulties of obtaining bat guano in deep caves and possible interpretational concerns relating to behaviour and feeding habits of different bat species, this material can be very useful in palaeoecological research provided that the dung was fossilized under favourable environmental conditions that allowed the preservation of pollen.     

Taxonomic considerations of Bartonella bacilliformis based on phylogenetic and phenotypic characteristics

The 16S-rRNA gene of Bartonella bacilliformis was amplified using the polymerase-chain reaction (PCR). The amplification product was sequenced using a linear-PCR procedure and compared with other published 16S-rRNA sequences. The results of this analysis placed B. bacilliformis in the alpha subgroup of the proteobacteria, and more specifically demonstrated its close phylogenetic relationship to Rochalimaea quintana. This relationship is supported by similarities in the size and mean base composition of the genomes of the two species, and by shared phenotypic characteristics.     

A phylogenetic analysis based on the gene encoding phosphoglycerate kinase

Summary We have determined the nucleotide sequence of both genomic and complementary DNA (cDNA) for the gene encoding the glycolytic enzyme phosphoglycerate kinase from the ciliated protozoan Tetrahymena thermophila. The amino acid sequence for the enzyme has also been derived from the cDNA sequence. The gene contains an open reading frame of 1260 nucleotides encoding 420 amino acids. Coding sequence in genomic DNA is interrupted by two introns at positions corresponding to introns 3 and 4 in mammalian phosphoglycerate kinase genes. The derived amino acid sequence was used to prepare a phylogeny by aligning the Tetrahymena sequence with 25 other phosphoglycerate kinase amino acid sequences. The Tetrahymena sequence is a typical eukaryotic sequence. There is recognizable and clear homology across species that cover nearly the complete range of life forms. The phylogenetic reconstruction of these sequences generally supports the conclusions that have been reached using rRNA sequences.Offprint requests to: R.E. Pearlman     

RFLP analysis of phylogenetic relationships and genetic variation in the genus Lycopersicon

Summary Forty single-copy, nuclear probes of known chromosomal position were used to examine restriction fragment length polymorphism in the tomato genus Lycopersion. The probes were from three libraries: one cDNA, and two genomic libraries ne genomic made with EcoRI and the other with PstI. Total DNA from 156 plants representing eight species was cut with five different restriction enzymes and scored in 198 probe-enzyme combinations. Genetic distances between accessions (populations) and species were calculated from the resultant restriction patterns and proportion of shared bands. Accessions belonging to the same species largely clustered together, confirming their current classification. However, one mountain accession, classified as L. peruvianum var. humifusum (LA2150), was sufficiently distinct from the other accessions of L. peruvianum that it may qualify as a separate species L. esculentum and L. pimpinellifolium were the least clearly differentiated, possibly reflecting introgressive hybridization, known to have been promoted by man in recent history. Dendrograms constructed from cDNA versus genomic clones were nearly identical in their general grouping of species. The dendrograms revealed two major dichotomies in the genus: one corresponding to mating behavior [self-compatible (SC) versus self-incompatible (SI) species] and the other corresponding to fruit color (red versus green-fruited species). The ratio of withinversus between-accession diversity was much lower for SC species, indicating that most of the diversity within these species exists between populations, rather than within populations. Overall, the amount of genetic variation in the SI species far exceeded that found in SC species. This result is exemplified by the fact that more genetic variation could be found within a single accession of one of the SI species (e.g., L. peruvianum) than among all accessions tested of any one of the SC species (e.g., L. esculentum or L. pimpinellifolium). Results from this study are discussed in relationship to germ plasm collection/utilization and with regard to the use of RFLPs in tomato breeding and genetics.     

A phylogenetic analysis of the aureoidSenecio (Asteraceae) complex based on ITS sequence data

The internal transcribed spacer region of the 18S–25S nuclear ribosomal DNA repeat was sequenced from 28 populations of the aureoidSenecio complex as well as two populations from the Lugentes group and one from the Tephroseroid group. Divergence levels for populations within the aureoid complex are very low (0.0 to 4.1%). Phylogenetic trees generated from the sequence data provide no support for the recognition of Aurei, Tomentosi and Lobati subgroups within the aureoid complex. With two Lugentes and one Tephroseroid species as outgroups,Senecio glabellus is the sister group of the rest of the aureoids. The high level of divergence between the aureoids and the three outgroup species indicates that the Lugentes and the Tephroseroids may not be closely related to the aureoids.     

A phylogenetic analysis of the genus Leuconostoc based on reverse transcriptase sequencing of 16 S rRNA

The phylogenetic interrelationships of members of the genus Leuconostoc and some heterofermentative lactobacilli, which phenotypically resemble leuconostocs, were investigated by comparative analysis of their 16 S rRNA sequences. The six species, Leuconostoc mesenteroides, Leu. carnosum, Leu. citreum, Leu. gelidum, Leu. lactis and Leu. pseudomesenteroides exhibited a high degree of sequence similarity with each other and formed a phylogenetically coherent group, quite separate from all other lactic acid bacteria investigated. The species Leu. paramesenteroides was found to be phylogenetically distinct from the Leu. mesenteroides group of species and formed a natural grouping with the heterofermentative lactobacilli, Lb. confusus, Lb. kandleri, Lb. minor and Lb. viridescens. The rRNA sequence of the acidophilic species, Leu. oenos, displayed exceptionally low levels of homology with all of the other taxa examined. The 16 S sequence of Leu. oenos showed major nucleotide differences in relatively highly conserved positions of the molecule indicating this species is phylogenetically distinct and warrants a separate genus.     

Utility of arginine kinase for resolution of phylogenetic relationships among Brachyuran genera and families

The molecular phylogenetics of decapod crustaceans has been based on sequence data from a limited number of genes. These have included rapidly evolving mitochondrial genes, which are most appropriate for studies of closely related species, and slowly evolving nuclear ribosomal RNA genes, which have been most useful for resolution of deep branches within the Decapoda. Here we examine the utility of the nuclear gene that encodes arginine kinase for phylogenetic reconstruction at intermediate levels (relationships among genera and families) within the decapod infraorder Brachyura (the true crabs). Analyses based on arginine kinase sequences were compared and combined with those for the mitochondrial cytochrome oxidase I gene. All of the genera in our taxon sample were resolved with high support with arginine kinase data alone. However, some of these genera were grouped into clades that are in conflict with recognized brachyuran families. A phylogeny based on cytochrome oxidase I was consistent with the arginine kinase phylogeny, but with weaker support. A recently proposed measure of phylogenetic informativeness indicated that arginine kinase was generally more informative than cytochrome oxidase I for relationships above the level of genus. Combined analysis of data from both genes provided strong support for clades that are in conflict with current assignments of genera to the families Epialtidae, Mithracidae, Pisidae, and Portunidae.     

The evolution of virulence in primate malaria parasites based on Bayesian reconstructions of ancestral states

Plasmodium parasites, the causative agents of malaria, are generally considered as harmful parasites, but many of them cause mild symptoms. Little is known about the evolutionary history and phylogenetic constraints that generate this interspecific variation in virulence due to uncertainties about the phylogenetic associations of parasites. Here, to account for such phylogenetic uncertainty, phylogenetic methods based on Bayesian statistics were followed in combination with sequence data from five genes to estimate the ancestral state of virulence in primate Plasmodium parasites. When recent parasites were categorised according to the damage caused to the host, Bayesian estimates of ancestral states indicated that the acquisition of a harmful host exploitation strategy is more likely to be a recent evolutionary event than a result of an ancient change in a character state altering virulence. On the contrary, there was more evidence for moderate host exploitation having a deep origin along the phylogenetic tree. Moreover, the evolution of host severity is determined by the phylogenetic relationships of parasites, as severity gains did not appear randomly on the evolutionary tree. Such phylogenetic constraints can be mediated by the acquisition of virulence genes. As the impact of a parasite on a host is the result of both the parasite’s investment in reproduction and host sensitivity, virulence was also estimated by calculating peak parasitemia after eliminating host effects. A directional random-walk evolutionary model showed that the ancestral primate malarias reproduced at very low parasitemia in their hosts. Consequently, the extreme variation in the outcome of malaria infection in different host species can be better understood in light of the phylogeny of parasites.     

The phylogenetic position of the Aeolosomatidae and Parergodrilidae, two enigmatic oligochaete-like taxa of the 'Polychaeta', based on molecular data from 18S rDNA sequences

The Aeolosomatidae and the Parergodrilidae are meiofaunal Annelida showing different combinations of clitellate‐like and non‐clitellate character states. Their phylogenetic positions and their systematic status within the Annelida are still in debate. Here we attempt to infer their systematic position using 18S rDNA sequences of the aeolosomatid Aeolosoma sp. and the parergodrilid Stygocapitella subterranea and several other meiofaunal taxa such as the Dinophilidae, Polygordiidae and Saccocirridae. The data matrix was complemented by sequences from several annelid, arthropod and molluscan species. After evaluation of the phylogenetic signal the data set was analysed with maximum‐parsimony, distance and maximum‐likelihood algorithms. Sequences from selected arthropods or molluscs were chosen for outgroup comparison. The resolution of the resulting phylogenies is discussed in comparison to previous studies. The results do not unequivocally support a sister‐group relationship of Aeolosoma sp. and the Clitellata. Instead, depending on the algorithms applied, Aeolosoma clusters in various clades within the polychaetes, for instance, together with eunicidan species, the Dinophilidae, Harmothoë impar or Nereis limbata. The position of Aeolosoma sp. thus cannot be resolved on the basis of the data available. S. subterranea always falls close to a cluster comprising Scoloplos armiger, Questa paucibranchiata and Magelona mirabilis, all of which were resolved as not closely related to both Aeolosoma sp. and the Clitellata. Therefore, convergent evolution of clitellate‐like characters in S. subterranea and hence in the Parergodrilidae is suggested by our phylogenetic analysis. Moreover, the Clitellata form a monophyletic clade within the paraphyletic polychaetes.     

Identification of the horizontal gene transfer based on phylogenetic data

We suggest a new procedure to search for the genes with horizontal transfer events in their evolutionary history. The search is based on analysis of topology difference between the phylogenetic trees of gene (protein) groups and the corresponding phylogenetic species trees. Numeric values are introduced to measure the discrepancy between the trees. This approach was applied to analyze 40 prokaryotic genomes classified into 132 classes of orthologs. This resulted in a list of the candidate genes for which the hypothesis of horizontal transfer in evolution looks true.     

A phylogenetic hypothesis for Asilidae based on a total evidence analysis of morphological and DNA sequence data (Insecta: Diptera: Brachycera: Asiloidea)

An hypothesis of phylogenetic relationships of Asilidae and its constituent taxa is presented, combining morphological and DNA sequence data in a total evidence framework. It is based on 77 robber fly species, 11 Asiloidea outgroup species, 211 morphological characters of the adult fly, and approximately 7300 bp of nuclear DNA from five genes (18S and 28S rDNA, AATS, CAD, and EF-1α protein-encoding DNA). The equally weighted, simultaneous parsimony analysis under dynamic homology in POY resulted in a single most parsimonious cladogram with a cost of 27,582 (iterative pass optimization; 27,703 under regular direct optimization). Six of the 12 included subfamily taxa are recovered as monophyletic. Trigonomiminae, previously always considered as monophyletic based on morphology, is shown to be non-monophyletic. Two of the three Trigonomiminae genera, Holcocephala Jaennicke, 1867 and Rhipidocephala Hermann, 1926, group unexpectedly as the sister taxon to all other Asilidae. Laphriinae, previously seen in the latter position, is the sister group of the remaining Asilidae. Five other subfamily taxa, i.e. Brachyrhopalinae, Dasypogoninae, Stenopogoninae, Tillobromatinae, and Willistonininae, are also shown to be non-monophyletic. The phylogenetic relationships among the higher-level taxa are partly at odds with findings of a recently published morphological study based on more extensive taxon sampling. The total evidence hypothesis is considered as the most informative one, but the respective topologies from the total-evidence, morphology-only, and molecular-only analyses are compared and contrasted in order to discuss the signals from morphological versus molecular data, and to analyze whether the molecular data outcompete the fewer morphological characters. A clade Apioceridae+Mydidae is corroborated as the sister taxon to Asilidae.     

Increasing the data size to accurately reconstruct the phylogenetic relationships between nine subgroups of the Drosophila melanogaster species group (Drosophilidae, Diptera)

Previous phylogenetic analyses of the melanogaster species group have led to conflicting hypotheses concerning their relationship; therefore the addition of new sequence data is necessary to discover the phylogeny of this species group. Here we present new data derived from 17 genes and representing 48 species to reconstruct the phylogeny of the melanogaster group. A variety of statistical tests, as well as maximum likelihood mapping analysis, were performed to estimate data quality, suggesting that all genes had a high degree of contribution to resolve the phylogeny.Individual locus was analyzed using maximum likelihood (ML), and the concatenated dataset (12,988 bp) were analyzed using partitioned maximum likelihood (ML) and Bayesian analyses. Separated analysis produced various phylogenetic relationships, however, phylogenetic topologies from ML and Bayesian analysis based on concatenated dataset, at the subgroup level, were completely identical to each other with high levels of support. Our results recovered three major clades: the ananassae subgroup, followed by the montium subgroup, the melanogaster subgroup and the oriental subgroups form the third monophyletic clade, in which melanogaster (takahashii, suzukii) forms one subclade and ficusphila [eugracilis (elegans, rhopaloa)] forms another. However, more data are necessary to determine the phylogenetic position of Drosophila lucipennis which proved difficult to place.     

Improved phylogenetic resolution of toxic and non-toxic Alexandrium strains using a concatenated rDNA approach

Dinoflagellates of the genus Alexandrium are known producers of paralytic shellfish toxins. Species within the genus have similar phenotypes making morphological identification problematical. The use of Alexandrium rDNA sequence data is therefore increasing, resulting in the improved resolution of evolutionary relationships by phylogenetic inferences. However, the true branching pattern within Alexandrium remains unresolved, with minimal support shown for the main phylogentic branch. The aim of this study is to improve phylogenetic resolution via a concatenated rDNA approach with a broad sample of taxa, allowing inference of the evolutionary pattern between species and toxins. 27 Alexandrium strains from 10 species were tested with HPLC for PSP toxin presence and additionally sequenced for 18S, ITS1, 5.8S, ITS2 and 28S rDNA before being phylogenetically inferred together with all available orthologous sequences from NCBI. The resulting alignment is the largest to date for the genus, in terms of both inferred characters and taxa, thus allowing for the improved phylogenetic resolution of evolutionary patterns there in. No phylogenetic pattern between PSP producing and non-producing strains could be established, however the terminal tamarense complex was shown to produce more PSP analogues than basal clades. Additionally, we distinguish a high number of polymorphic regions between the two copies of A. fundyense rDNA, thus allowing us to demonstrate the presence of chimeric sequences within GenBank, as well as a possible over estimation of diversification within the tamarense complex.     

The phylogenetic position of Hydrogenobacter acidophilus based on 16S rRNA sequence analysis

Abstract Hydrogenobacter acidophilus strain 3H-1 is a thermoacidophilic, obligately chemolithoautotrophic, hydrogen-oxidizer isolated from a Japanese solfataric field. Strain 3H-1 requires elemental sulfur for growth. We used PCR to amplify the 16S rRNA gene of strain 3H-1, and sequenced the amplification product directly. Phylogenetic analyses show strain 3H-1 is closely related to Aquifex pyrophilus and may be located in the deepest branch within the eubacterial phylogenetic tree. Sulfur-dependency of the ancestral eubacterium is also discussed.     

Phylogeny of the owlet-nightjars (Aves: Aegothelidae) based on mitochondrial DNA sequence

The avian family Aegothelidae (Owlet-nightjars) comprises nine extant species and one extinct species, all of which are currently classified in a single genus, Aegotheles. Owlet-nightjars are secretive nocturnal birds of the South Pacific. They are relatively poorly studied and some species are known from only a few specimens. Furthermore, their confusing morphological variation has made it difficult to cluster existing specimens unambiguously into hierarchical taxonomic units. Here we sample all extant owlet-nightjar species and all but three currently recognized subspecies. We use DNA extracted primarily from museum specimens to obtain mitochondrial gene sequences and construct a molecular phylogeny. Our phylogeny suggests that most species are reciprocally monophyletic, however A. albertisi appears paraphyletic. Our data also suggest splitting A. bennettii into two species and splitting A. insignis and A. tatei as suggested in another recent paper.