Higher-level Phylogeny Research Articles

Two mitochondrial genomes from the families Bethylidae and Mutillidae: Independent rearrangement of protein-coding genes and higher-level phylogeny of the Hymenoptera

In animal mitochondrial genomes, gene arrangements are usually conserved across major lineages but might be rearranged within derived groups, and might provide valuable phylogenetic characters. Here, we sequenced the mitochondrial genomes of Cephalonomia gallicola (Chrysidoidea: Bethylidae) and Wallacidia oculata (Vespoidea: Mutillidae). In Cephalonomia at least 11 tRNA and 2 protein-coding genes were rearranged, which is the first report of protein-coding gene rearrangements in the Aculeata. In the Hymenoptera, three types of protein-coding gene rearrangement events occur, i.e. reversal, transposition and reverse transposition. Venturia (Ichneumonidae) had the greatest number of common intervals with the ancestral gene arrangement pattern, whereas Philotrypesis (Agaonidae) had the fewest. The most similar rearrangement patterns are shared between Nasonia (Pteromalidae) and Philotrypesis, whereas the most differentiated rearrangements occur between Cotesia (Braconidae) and Philotrypesis. It is clear that protein-coding gene rearrangements in the Hymenoptera are evolutionarily independent across the major lineages but are conserved within groups such as the Chalcidoidea. Phylogenetic analyses supported the sister-group relationship of Orrussoidea and Apocrita, Ichneumonoidea and Aculeata, Vespidae and Apoidea, and the paraphyly of Vespoidea. The Evaniomorpha and phylogenetic relationships within Aculeata remain controversial, with discrepancy between analyses using protein-coding and RNA genes.

Higher level molecular phylogeny of darkling beetles (Coleoptera:Tenebrionidae)

AbstractInsect diversity represents about 60% of the estimated million‐and‐a‐half described eukaryotic species worldwide, yet comprehensive and well‐resolved intra‐ordinal phylogenies are still lacking for the majority of insect groups. This is the case especially for the most species‐rich insect group, the beetles (Coleoptera), a group for which less than 4% of the known species have had theirDNAsequenced. In this study, we reconstruct the first higher level phylogeny based onDNAsequence data for the species‐rich darkling beetles, a family comprising at least 20 000 species. Although amongst all families of beetlesTenebrionidae ranks seventh in terms of species diversity, the lack of knowledge on the phylogeny and systematics of the group is such that its monophyly has been questioned (not to mention those of the subfamilies and tribes contained within it). We investigate the evolutionary history ofTenebrionidae using multiple phylogenetic inference methods (Bayesian inference, maximum likelihood and parsimony) to analyse a dataset consisting of eight gene fragments across 404 taxa (including 250 tenebrionid species). Although the resulting phylogenetic framework only encompasses a fraction of the known tenebrionid diversity, it provides important information on their systematics and evolution. Whatever the methods used, our results provide strong support for the monophyly of the family, and highlight the likely paraphyletic or polyphyletic nature of several important tenebrionid subfamilies and tribes, notably the polyphyletic subfamiliesDiaperinae andTenebrioninae that clearly require substantial revision in the future. Some interesting associations in several groups are also revealed by the phylogenetic analyses, such as the pairing ofAphtoraBates withPhrenapatinae. Furthermore this study advances our knowledge of the evolution of the group, providing novel insights into much‐debated theories, such as the apparent relict distribution of the tribeElenophorini.

Phylogeny drives large scale patterns in Australian marine bioactivity and provides a new chemical ecology rationale for future biodiscovery.

Twenty-five years of Australian marine bioresources collecting and research by the Australian Institute of Marine Science (AIMS) has explored the breadth of latitudinally and longitudinally diverse marine habitats that comprise Australia’s ocean territory. The resulting AIMS Bioresources Library and associated relational database integrate biodiversity with bioactivity data, and these resources were mined to retrospectively assess biogeographic, taxonomic and phylogenetic patterns in cytotoxic, antimicrobial, and central nervous system (CNS)-protective bioactivity. While the bioassays used were originally chosen to be indicative of pharmaceutically relevant bioactivity, the results have qualified ecological relevance regarding secondary metabolism. In general, metazoan phyla along the deuterostome phylogenetic pathway (eg to Chordata) and their ancestors (eg Porifera and Cnidaria) had higher percentages of bioactive samples in the assays examined. While taxonomy at the phylum level and higher-order phylogeny groupings helped account for observed trends, taxonomy to genus did not resolve the trends any further. In addition, the results did not identify any biogeographic bioactivity hotspots that correlated with biodiversity hotspots. We conclude with a hypothesis that high-level phylogeny, and therefore the metabolic machinery available to an organism, is a major determinant of bioactivity, while habitat diversity and ecological circumstance are possible drivers in the activation of this machinery and bioactive secondary metabolism. This study supports the strategy of targeting phyla from the deuterostome lineage (including ancestral phyla) from biodiverse marine habitats and ecological niches, in future biodiscovery, at least that which is focused on vertebrate (including human) health.

A molecular analysis of the Gelechiidae (Lepidoptera, Gelechioidea) with an interpretative grouping of its taxa

We re‐examine the higher level phylogeny and evolutionary affinities of the family Gelechiidae (Lepidoptera: Gelechioidea) based on DNA sequence data for one mitochondrial gene (cytochrome c oxidase subunit I) and seven nuclear genes (Elongation Factor‐1α,wingless,Ribosomal protein S5,Isocitrate dehydrogenase,Cytosolic malate dehydrogenase,Glyceraldehyde‐3‐phosphate dehydrogenaseandCarbamoylphosphate synthase domain protein). Fifty‐two taxa representing nearly all established subfamilies and tribes of Gelechiidae, and about 10% of described gelechiid genera, in addition to five outgroup taxa were sequenced. Data matrices (6157 bp total) were analysed under model‐based evolutionary methods (Maximum Likelihood and Bayesian Inference), resulting in novel high‐level phylogenetic interrelationships. The best supported cladogram divided the Gelechiidae into six distinct clades corresponding to the subfamilies Anacampsinae, Dichomeridinae, Apatetrinae, Thiotrichinae, Anomologinae and Gelechiinae (+ Physoptilinae, which were not available for study). The results suggest the following adjustments in gelechiid interrelationships: Brachmini is nested within Dichomeridinae; Anarsiini is the sister group of Chelariini; Pexicopiinae is the sister group of Apatetrinae, here suggested to be treated as a tribe Pexicopiini of Apatetrinae. A new subfamily Thiotrichinae (subfam.n.) is proposed on the basis of the resurrected genusThiotrichaMeyrick (gen.rev.), which includesMacrenchesMeyrick,PalumbinaRondani andPolyhymnoChambers. Gelechiidae display a wide array of life‐history strategies, but the diversity in patterns of larval mode of life has direct phylogenetic correlation only below subfamily level, suggesting multiple origins and/or frequent reversals for traits such as external or internal feeding and leaf mining within the family.

First comparative study of primate morphological and molecular evolutionary rates including muscle data: implications for the tempo and mode of primate and human evolution.

Here we provide the first report about the rates of muscle evolution derived from Bayesian and parsimony cladistic analyses of primate higher-level phylogeny, and compare these rates with published rates of molecular evolution. It is commonly accepted that there is a 'general molecular slow-down of hominoids', but interestingly the rates of muscle evolution in the nodes leading and within the hominoid clade are higher than those in the vast majority of other primate clades. The rate of muscle evolution at the node leading to Homo (1.77) is higher than that at the nodes leading to Pan (0.89) and particularly to Gorilla (0.28). Notably, the rates of muscle evolution at the major euarchontan and primate nodes are different, but within each major primate clade (Strepsirrhini, Platyrrhini, Cercopithecidae and Hominoidea) the rates at the various nodes, and particularly at the nodes leading to the higher groups (i.e. including more than one genera), are strikingly similar. We explore the implications of these new data for the tempo and mode of primate and human evolution.

A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes.

BackgroundThe extant squamates (>9400 known species of lizards and snakes) are one of the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and to address their classification. Here, we present the first large-scale phylogenetic estimate for Squamata.ResultsThe estimated phylogeny contains 4161 species, representing all currently recognized families and subfamilies. The analysis is based on up to 12896 base pairs of sequence data per species (average = 2497 bp) from 12 genes, including seven nuclear loci (BDNF, c-mos, NT3, PDC, R35, RAG-1, and RAG-2), and five mitochondrial genes (12S, 16S, cytochrome b, ND2, and ND4). The tree provides important confirmation for recent estimates of higher-level squamate phylogeny based on molecular data (but with more limited taxon sampling), estimates that are very different from previous morphology-based hypotheses. The tree also includes many relationships that differ from previous molecular estimates and many that differ from traditional taxonomy.ConclusionsWe present a new large-scale phylogeny of squamate reptiles that should be a valuable resource for future comparative studies. We also present a revised classification of squamates at the family and subfamily level to bring the taxonomy more in line with the new phylogenetic hypothesis. This classification includes new, resurrected, and modified subfamilies within gymnophthalmid and scincid lizards, and boid, colubrid, and lamprophiid snakes.

Summary of Laurasiatheria (Mammalia) Phylogeny

Laurasiatheria is one of the richest and most diverse superorders of placental mammals. Because this group had a rapid evolutionary radiation, the phylogenetic relationships among the six orders of Laurasiatheria remain a subject of heated debate and several issues related to its phylogeny remain open. Reconstructing the true phylogenetic relationships of Laurasiatheria is a significant case study in evolutionary biology due to the diversity of this suborder and such research will have significant implications for biodiversity conservation. We review the higher-level (inter-ordinal) phylogenies of Laurasiatheria based on previous cytogenetic, morphological and molecular data, and discuss the controversies of its phylogenetic relationship. This review aims to outline future researches on Laurasiatheria phylogeny and adaptive evolution.

Estimating Speciation and Extinction Rates for Phylogenies of Higher Taxa

Speciation and extinction rates can be estimated from molecular phylogenies. Recently, a number of methods have been published showing that these rates can be estimated even if the phylogeny is incomplete, that is, if not all extant species are included. We show that the accuracy of such methods strongly depends on making the correct assumptions about how the sampling process was performed. We focus on phylogenies that are incomplete because some subclades (e.g., genera and families) are each represented as a single lineage. We show that previous methods implicitly assumed that such subclades are defined by randomly (or in an extreme deterministic way) choosing the edges that define the subclades from the complete species phylogeny. We show that these methods produce biased results if higher taxa are defined in a different manner. We introduce strict higher level phylogenies where subclades are defined so that the phylogeny is fully resolved from its origin to time x(cut), and fully unresolved thereafter, so that for all subclades, stem age > x(cut) > crown age. We present estimates of speciation and extinction rates from a phylogeny of birds in which this subclade definition was applied. However, for most higher level phylogenies in the literature, it is unclear how higher taxa were defined, but often such phylogenies can be easily transformed into strict higher level phylogenies, as we illustrate by estimating speciation and extinction rates from a near-complete but only partly resolved species-level phylogeny of mammals. The accuracy of our methods is verified using simulations.

Resolving discrepancy between nucleotides and amino acids in deep-level arthropod phylogenomics: differentiating serine codons in 21-amino-acid models.

BackgroundIn a previous study of higher-level arthropod phylogeny, analyses of nucleotide sequences from 62 protein-coding nuclear genes for 80 panarthopod species yielded significantly higher bootstrap support for selected nodes than did amino acids. This study investigates the cause of that discrepancy.Methodology/Principal FindingsThe hypothesis is tested that failure to distinguish the serine residues encoded by two disjunct clusters of codons (TCN, AGY) in amino acid analyses leads to this discrepancy. In one test, the two clusters of serine codons (Ser1, Ser2) are conceptually translated as separate amino acids. Analysis of the resulting 21-amino-acid data matrix shows striking increases in bootstrap support, in some cases matching that in nucleotide analyses. In a second approach, nucleotide and 20-amino-acid data sets are artificially altered through targeted deletions, modifications, and replacements, revealing the pivotal contributions of distinct Ser1 and Ser2 codons. We confirm that previous methods of coding nonsynonymous nucleotide change are robust and computationally efficient by introducing two new degeneracy coding methods. We demonstrate for degeneracy coding that neither compositional heterogeneity at the level of nucleotides nor codon usage bias between Ser1 and Ser2 clusters of codons (or their separately coded amino acids) is a major source of non-phylogenetic signal.ConclusionsThe incongruity in support between amino-acid and nucleotide analyses of the forementioned arthropod data set is resolved by showing that “standard” 20-amino-acid analyses yield lower node support specifically when serine provides crucial signal. Separate coding of Ser1 and Ser2 residues yields support commensurate with that found by degenerated nucleotides, without introducing phylogenetic artifacts. While exclusion of all serine data leads to reduced support for serine-sensitive nodes, these nodes are still recovered in the ML topology, indicating that the enhanced signal from Ser1 and Ser2 is not qualitatively different from that of the other amino acids.

Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species

Squamate reptiles (lizards and snakes) are one of the most diverse groups of terrestrial vertebrates. Recent molecular analyses have suggested a very different squamate phylogeny relative to morphological hypotheses, but many aspects remain uncertain from molecular data. Here, we analyse higher-level squamate phylogeny with a molecular dataset of unprecedented size, including 161 squamate species for up to 44 nuclear genes each (33 717 base pairs), using both concatenated and species-tree methods for the first time. Our results strongly resolve most squamate relationships and reveal some surprising results. In contrast to most other recent studies, we find that dibamids and gekkotans are together the sister group to all other squamates. Remarkably, we find that the distinctive scolecophidians (blind snakes) are paraphyletic with respect to other snakes, suggesting that snakes were primitively burrowers and subsequently re-invaded surface habitats. Finally, we find that some clades remain poorly supported, despite our extensive data. Our analyses show that weakly supported clades are associated with relatively short branches for which individual genes often show conflicting relationships. These latter results have important implications for all studies that attempt to resolve phylogenies with large-scale phylogenomic datasets.

Progress report on the study of wood-decaying fungi in China

This study addressed three important aims: (1) undermining the previously obtained raw data about wood-decaying fungi (WDF) distribution and continuously investigating permanent plots to address certain scientific questions in ecology, (2) resolving the higher-level phylogeny of WDF with the help of multiple loci, and (3) testing and estimating the medicinal values of species that are closely related to well-known medicinal species. More than 1200 species and 2469 strains of WDF in China were identified from 28908 specimens collected from a series of field investigations. Using these materials, studies in multiple disciplines, such as ecology, taxonomy and phylogeny, and medicine, have been performed. With respect to ecology, the diversity of wood-decaying polypores significantly differed among a boreal forest zone, a temperate and warm temperate forest zone, and a tropical and subtropical forest zone. For instance, from north to south, the number and proportion of brown-rot species and the proportion of species found on fallen trunks were both decreased. The ecological patterns of wood-decaying polypores on gymnosperm and angiosperm trees were also explored by a case study in Northeast China. Although the total species richness was similar between the two tree groups, several other characteristics were significantly different, such as community structure and richness in certain substrates. The taxonomy and phylogeny of wide samples were referred to and their phylogenetic positions were resolved or at least partially established. In particular, phylogenetic knowledge about four genera, Fomitiporia, Ganoderma, Inonotus and Perenniporia, which include medicinal species, was essential for further research to determine the medicinal values of these types of fungi. Among these medicinal species, we mainly focused on Inonotus obliquus for its medicinal purposes. Polyphenols, polysaccharides and lanostane-type triterpenoids, extracted from the sterile conk of this species, could dramatically decrease levels of free radicals, DPPH and hydroxyl radicals, respectively. The metabolic profiles (both production and composition) of cultured I. obliquus mycelia could be altered by co-culture with other medicinal species or by induction of S-nitrosylation and denitrosylation, which may enhance the antioxidant capacity of I. obliquus.

Ternatus, a new spider genus from China with a cladistic analysis and comments on its phylogenetic placement (Araneae: Linyphiidae)

A new spider genus, Ternatus n. gen., is erected to accommodate two new erigonine species from China, Ternatus malleatusn. sp. and Ternatus siculus n. sp. Descriptions and illustrations of the new genus and new species are provided. To test the phy-logenetic placement within Linyphiidae, morphological data of the two new species were added to the matrices of two previousstudies addressing the higher level phylogeny of erigonine spiders. The results of the cladistic analyses support the monophyly of the new genus and its sister group relationship to the genus Gonatium Menge, 1868.

Burseraceae: a model for studying the Amazon flora

A well-studied group of plants can serve as a model for addressing issues in conservation, evolution, and biogeography, making it possible to assign conservation status with confidence and detecting not only those taxa that are most threatened but also those that represent basal, unique, and/or relictual members of entire lineages. Clarified higher-level phylogenetic relationships open the door to more refined systematics of clades without having to worry if they are para- or polyphyletic. A well-studied group can also be an excellent testing ground for new or under-utilized tools and independent data sets. Research on the Burseraceae, with over 100 taxa in the Amazon, is rapidly arriving at the point where the family can be used effectively both as a tool for conservation and as a model for studying the processes influencing the origin and maintenance of high diversity in the Amazonian flora. First, we are resolving higher-level phylogenies as well as species-level taxonomy in various clades, allowing comparative approaches. Second, the family occurs throughout Amazonia and is well-represented in most habitats overall, but most of the taxa are restricted in their distributions and/or habitats; this makes it possible to test the relative importance of geographic barriers vs. habitat diversity in the speciation process. The family is sufficiently large to provide adequate statistical power for hypothesis testing and yet small enough to achieve the necessary sampling intensity, allowing us to assess the relative impacts of morphological innovation, ecological opportunity, and biogeographic events on the diversification of Burseraceae and related groups.

AreMonobiaandMontezumiaMonophyletic? A Cladistic Analysis of their Species Groups Based on Morphological Data (Hymenoptera, Vespidae, Eumeninae)

A concept of the higher-level phylogeny of the Eumeninae remains elusive. As such, the naturalness of several genera occurring in the Neotropical region is doubtful, including Monobia and Montezumia. Morphological data were used to infer the phylogenetic relationships among the species groups within both genera, as well as to test their monophyly. Analyses recovered Monobia and Montezumia as monophyletic as long as Montezumia arizonensis and Montezumia aurata were included in Monobia. Most species groups proposed by Willink in 1982 were also recovered as monophyletic. Three new combinations are proposed in congruence with the phylogenetic results: Monobia arizonensis, new combination, Monobia aurata, revised combination, and Monobia oaxaca, new combination. An additional new species is described: Monobia goiana Hermes, new species.

A Comparative Study of Mammalian Diversification Pattern

Although mammals have long been regarded as a successful radiation, the diversification pattern among the clades is still poorly known. Higher-level phylogenies are conflicting and comprehensive comparative analyses are still lacking. Using a recently published supermatrix encompassing nearly all extant mammalian families and a novel comparative likelihood approach (MEDUSA), the diversification pattern of mammalian groups was examined. Both order- and family-level phylogenetic analyses revealed the rapid radiation of Boreoeutheria and Euaustralidelphia in the early mammalian history. The observation of a diversification burst within Boreoeutheria at approximately 100 My supports the Long Fuse model in elucidating placental diversification progress, and the rapid radiation of Euaustralidelphia suggests an important role of biogeographic dispersal events in triggering early Australian marsupial rapid radiation. Diversification analyses based on family-level diversity tree revealed seven additional clades with exceptional diversification rate shifts, six of which represent accelerations in net diversification rate as compared to the background pattern. The shifts gave origin to the clades Muridae+Cricetidae, Bovidae+Moschidae+Cervidae, Simiiformes, Echimyidae, Odontoceti (excluding Physeteridae+Kogiidae+Platanistidae), Macropodidae, and Vespertilionidae. Moderate to high extinction rates from background and boreoeutherian diversification patterns indicate the important role of turnovers in shaping the heterogeneous taxonomic richness observed among extant mammalian groups. Furthermore, the present results emphasize the key role of extinction on erasing unusual diversification signals, and suggest that further studies are needed to clarify the historical radiation of some mammalian groups for which MEDUSA did not detect exceptional diversification rates.

Estimates of nuclear DNA content in red algal lineages.

The red algae are an evolutionarily ancient group of predominantly marine organisms with an estimated 6000 species. Consensus higher-level molecular phylogenies support a basal split between the unicellular Cyanidiophytina and morphologically diverse Rhodophytina, the later subphylum containing most red algal species. The Rhodophytina is divided into six classes, of which five represent early diverging lineages of generally uninucleate species, whose evolutionary relationships are poorly resolved. The remaining species compose the large (27 currently recognized orders), morphologically diverse and typically multinucleate Florideophyceae. Nuclear DNA content estimates have been published for <1 % of the described red algae. The present investigation summarizes the state of our knowledge and expands our coverage of DNA content information from 196 isolates of red algae. The DNA-localizing fluorochrome DAPI (4',6-diamidino-2-phenylindole) and RBC (chicken erythrocytes) standards were used to estimate 2C values with static microspectrophotometry. Nuclear DNA contents are reported for 196 isolates of red algae, almost doubling the number of estimates available for these organisms. Present results also confirm the reported DNA content range of 0.1-2.8 pg, with species of Ceramiales, Nemaliales and Palmariales containing apparently polyploid genomes with 2C = 2.8, 2.3 and 2.8 pg, respectively. Early diverging red algal lineages are characterized by relatively small 2C DNA contents while a wide range of 2C values is found within the derived Florideophyceae. An overall correlation between phylogenetic placement and 2C DNA content is not apparent; however, genome size data are available for only a small portion of red algae. Current data do support polyploidy and aneuploidy as pervasive features of red algal genome evolution.

Sources of signal in 62 protein-coding nuclear genes for higher-level phylogenetics of arthropods.

BackgroundThis study aims to investigate the strength of various sources of phylogenetic information that led to recent seemingly robust conclusions about higher-level arthropod phylogeny and to assess the role of excluding or downweighting synonymous change for arriving at those conclusions.Methodology/Principal FindingsThe current study analyzes DNA sequences from 68 gene segments of 62 distinct protein-coding nuclear genes for 80 species. Gene segments analyzed individually support numerous nodes recovered in combined-gene analyses, but few of the higher-level nodes of greatest current interest. However, neither is there support for conflicting alternatives to these higher-level nodes. Gene segments with higher rates of nonsynonymous change tend to be more informative overall, but those with lower rates tend to provide stronger support for deeper nodes. Higher-level nodes with bootstrap values in the 80% – 99% range for the complete data matrix are markedly more sensitive to substantial drops in their bootstrap percentages after character subsampling than those with 100% bootstrap, suggesting that these nodes are likely not to have been strongly supported with many fewer data than in the full matrix. Data set partitioning of total data by (mostly) synonymous and (mostly) nonsynonymous change improves overall node support, but the result remains much inferior to analysis of (unpartitioned) nonsynonymous change alone. Clusters of genes with similar nonsynonymous rate properties (e.g., faster vs. slower) show some distinct patterns of node support but few conflicts. Synonymous change is shown to contribute little, if any, phylogenetic signal to the support of higher-level nodes, but it does contribute nonphylogenetic signal, probably through its underlying heterogeneous nucleotide composition. Analysis of seemingly conservative indels does not prove useful.ConclusionsGenerating a robust molecular higher-level phylogeny of Arthropoda is currently possible with large amounts of data and an exclusive reliance on nonsynonymous change.

Cenozoic mystery birds – on the phylogenetic affinities of bony‐toothed birds (Pelagornithidae)

Mayr, G. (2011) Cenozoic mystery birds – on the phylogenetic affinities of bony‐toothed birds (Pelagornithidae). —Zoologica Scripta, 40, 448–467.The extinct Cenozoic bony‐toothed birds (Pelagornithidae) are characterized by the occurrence of unique spiky projections of the osseous jaws and are among the most distinctive neornithine taxa. Earlier authors considered these marine birds to be most closely related to ‘Pelecaniformes’ or Procellariiformes, but recent phylogenetic analyses resulted in a sister group relationship to Anseriformes. This latter hypothesis was, however, coupled with a non‐monophyly of galloanserine or even neognathous birds, which is not supported by all other current analyses. The character evidence for anseriform affinities of pelagornithids is thus reassessed, and it is detailed that the alleged apomorphies cannot be upheld. Pelagornithids lack some key apomorphies of galloanserine birds, and analysis of 107 anatomical characters did not support anseriform affinities, but resulted in a sister group relationship between Pelagornithidae and Galloanseres. By retaining a monophyletic Galloanseres, this result is in better accordance with widely acknowledged hypotheses on the higher‐level phylogeny of birds. The (Pelagornithidae + Galloanseres) clade received, however, only weak bootstrap support, and some characters, such as the presence of an open frontoparietal suture, may even support a position of Pelagornithidae outside crown‐group Neognathae.

Diaporthaceae associated with root and crown rot of maize

Several isolates of coelomycetous fungi with pigmented conidia were consistently isolated from diseased roots of Zea mays in irrigated plots monitored in the KwaZulu-Natal Province of South Africa. Based on their morphology, these isolates could be identified as representative of Stenocarpella macrospora, S. maydis, and Phaeocytostroma ambiguum. Although species of Stenocarpella are well-known as causal agents of cob and stalk rot and leaf blight of maize in South Africa, the occurrence and importance of P. ambiguum is less well documented and understood. To determine the role of P. ambiguum as a root pathogen of maize, pathogenicity tests were conducted under glasshouse conditions at 18 °C night and 28 °C day temperatures using a pasteurised soil, river sand and perlite medium and a 0.5 % sand-bran inoculum. Based on these results, P. ambiguum was shown to be a primary pathogen of maize, but to be less virulent than the positive control, S. maydis. Furthermore, to clarify the higher-level phylogeny of these fungal genera, isolates were subjected to DNA sequencing of the nuclear ribosomal DNA (ITS & LSU). Partial gene sequences of the translation elongation factor 1-alpha gene were added to confirm the species monophyly. To resolve the generic placement of Phaeocytostroma, additional species such as P. sacchari, P. plurivorum and P. megalosporum were also added to the analysis. Based on these results, Stenocarpella and Phaeocytostroma were shown to be two well defined genera, belonging to Diaporthales, Diaporthaceae, being closely allied to Phomopsis (Diaporthe). All three genera were also observed to form alpha as well as beta conidia, and although this phenomenon is well documented for Phomopsis and Phaeocytostroma, it is a new observation for Stenocarpella. In spite of the differences in conidial pigmentation, no support could be obtained for polyphyly in Diaporthaceae, suggesting that as observed in Botryosphaeriaceae (Botryosphaeriales), conidial pigmentation is not informative at the family level in Diaporthales.

Temporal Lags and Overlap in the Diversification of Weevils and Flowering Plants: Recent Advances and Prospects for Additional Resolution

Weevils (superfamily Curculionoidea) are by all accounts unusually successful. There are ~62,OOO described extant species in 7 families1 and ~5,800 genera. However; most weevil species remain undescribed (Oberprieler et aI., 2007). More than 80% of weevil species belong to the family Curculionidae (Anderson, 1995). Weevils collectively feed on nearly all kinds of plants and plant parts, but most living species are specialist herbivores on angiosperms (flowering plants). All living weevil families are known from the Cretaceous fossil record (Oberprieler et aI., 2007). The earliest unequivocal fossil weevils, representatives of the family Nemonychidae, appear in the Late Jurassic (Gratshev & Zherikhin, 2003). These early weevils probably developed in the reproductive structures of gymnosperms, most likely conifers or cycads (Kuschel, 1983; Farrell, 1998; McKenna et aI., 2009). Host shifts to angiosperms have been shown to be associated with increased taxonomic diversity in weevils (Farrell, 1998). However, until recently. the role of angiosperms in weevil macroevolution was difficult to interpret due to the lack of a well-resolved higher-level phylogeny and corresponding methodologically robust molecular timetree for weevils. McKenna etal. (2009) presented a large-scale molecular phylogeny and timetree for weevils based on ~8 kilo bases of ONA sequence data from six genes (185,285, arginine kinase, elongation factor i-a, cytochrome oxidase I, and 165). These data were obtained from a sample of 135 weevil genera representing all families and subfamilies and most major tribes of the family Curculionidae. Outgroups included exemplars from seven subfamilies of Chrysomeloidea (the weevil sister group) (Farrell, 1998; Marvaldi et aI., 2009), and the rather more distantly related cucujoid Ericmodes sylvaticus (Philippi) (Protocucujidae). Node ages estimated from combined analyses of molecular and fossil data were consistent with diversification of weevils into most extant families on gymnosperms in the Jurassic, and colonization of early crown-group angiosperms during the subsequent Early Cretaceous. Massive diversification of angiosperm-as-