Templeton Test Research Articles

Cranial and post-cranial remains and phylogenetic relationships of the Gondwanan meiolaniform turtle Peligrochelys walshae from the Paleocene of Chubut, Argentina

AbstractPeligrochelys walshae is a meiolaniform turtle originally described based on four specimens represented by cranial remains found in the classic locality of Punta Peligro (Chubut, Argentina) in outcrops of the Salamanca Formation (Danian). Recent field work in the vicinity of Punta Peligro resulted in the discovery of almost 30 new specimens, represented by cranial and postcranial remains that can be assigned to P. walshae. In this contribution, we provide a detailed anatomical description of the new specimens, provide an emended diagnosis for the species, and explore its phylogenetic relationships based on all anatomical data available for the species. The new specimens bring valuable information about the anatomy of the skull and postcranium of P. walshae as well as for meiolaniforms in general. The 3D preservation of the skull bones allows us to provide a 3D reconstruction using novel techniques. The updated phylogenetic analysis confirms that P. walshae is part of the clade Meiolaniformes, which spans from the Early Cretaceous until the Holocene and contains the giant, horned turtles (Meiolaniidae). This phylogenetic analysis reinforces the previous hypothesis that the clade Meiolaniformes is dominated by Gondwanan taxa, but also includes some Laurasian representatives. Alternate phylogenetic positions of taxa included in Meiolaniformes in this analysis were tested using the Templeton test. The lineage leading to Peligrochelys walshae is the only meiolaniform non-meiolaniid lineage to have survived the K-Pg mass extinction; its study provides valuable information to evaluate the effects of the K-Pg extinction in turtles.

Phylogenomics of the plant family Araceae

The biogeography, chromosome number evolution, pollination biology and evolutionary history of the plant family Araceae have recently become much clearer (Cabrera et al., 2008; Chartier et al., 2013; Cusimano et al., 2011, 2012; Nauheimer et al., 2012). However, phylogenetic ambiguity near the root of the tree precludes answering questions about the early evolution of the family. We use Illumina sequencing technology and reference based assembly to resolve the remaining questions in the deep phylogeny of Araceae. We sampled 32 genera and obtained 7 from GenBank (including an outgroup), representing 42 of 44 major clades described in Cusimano et al. (2011). A subsequent phylogenomic analysis based on mitochondrial data was performed to test congruence between plastid and mitochondrial data for phylogenetic inference. Plastid sequences produced strongly supported phylogenies. In contrast, mitochondrial phylogenies were weakly supported and incongruent with chloroplast data (Templeton test, p⩽0.0001), although several smaller clades were recovered. New strongly-supported clades seen here are: (1) Anubias and Montrichardia, excluding Calla, form a clade that is sister to the Zantedeschia clade; (2) the South African genus Zantedeschia is sister to the Old World Anchomanes clade; and (3) within the Zantedeschia clade, Philodendron is sister to the rest. Calla and Schismatoglottis form a clade at the base of one of two major clades in Aroideae based on complete chloroplast sequences. Although statistical support is weak, morphological and cytological features support this topology.

MLSTest: Novel software for multi-locus sequence data analysis in eukaryotic organisms

Multi-locus sequence typing (MLST) is a frequently used genotyping method whose goal is the unambiguous assignment of microorganisms to genetic clusters. MLST typically involves analysis of DNA sequence results generated from several house-keeping gene loci. MLST remains the gold standard for molecular typing of many bacterial pathogens. Eukaryotic pathogens have also been the subject of MLST, however, few tools are available to deal with diploid sequence data. Here we present novel software for MLST data analysis tailored towards diploid Eukaryotes: MLSTest. This software meets various methods used in MLST and introduces some novel methodologies for the evaluation of the data set. In addition to construction of allelic profiles and basic clustering analysis, the MLSTest looks for network structures that suggest genetic exchange in BURST graphs. Additionally, it uses several simple methods for tree construction with the advantage of managing heterozygous or three-state sites. Additionally, the software analyses whether concatenation of fragments from different genes is suitable for the data set using different tests (bionj-incongruence length difference test, Templeton test). It evaluates how the incongruence is distributed across the tree using a variation of the localized incongruence length difference test based on a modified neighbour joining algorithm. We tested the last method in simulated datasets. We showed that is conservative (adequate type I error rate) and moderately to highly powerful as well as useful to localize incongruences in two bacterial and two eukaryotic MLST datasets. MLSTest was also designed for developing MLST schemes. It thus has tools to optimize locus combinations and to reduce the number of targets required for typing. MLSTest also analyses whether the discriminatory power of the typing scheme is increased by including more loci. We evaluated the software over simulated and real datasets from bacterial and eukaryotic microorganisms. The software is freely available at http://www.ipe.unsa.edu.ar/software.

Phylogeny, divergence times, and historical biogeography of New World Dryopteris (Dryopteridaceae)

Dryopteris is a large, cosmopolitan fern genus ideal for addressing questions about diversification, biogeography, hybridization, and polyploidy, which have historically been understudied in ferns. We constructed a highly resolved, well-supported phylogeny for New World Dryopteris and used it to investigate biogeographic patterns and divergence times. We analyzed relationships among 97 species of Dryopteris, including taxa from all major biogeographic regions, with analyses based on 5699 aligned nucleotides from seven plastid loci. Phylogenetic analyses used maximum parsimony, maximum likelihood, and Bayesian inference. We conducted divergence time analyses using BEAST and biogeographic analyses using maximum parsimony, maximum likelihood, Bayesian, and S-DIVA approaches. We explored the monophyly of subgenera and sections in the most recent generic classification and of geographic groups of taxa using Templeton tests. The genus Dryopteris arose ca. 42 million years ago (Ma). Most of the Central and South American species form a well-supported clade which arose 32 Ma, but the remaining New World species are the result of multiple, independent dispersal and vicariance events involving Asia, Europe, and Africa over the last 15 Myr. We identified six long-distance dispersal events and three vicariance events in the immediate ancestry of New World species; reconstructions for another four lineages were ambiguous. New World Dryopteris are not monophyletic; vicariance has dominated the history of the North American species, while long-distance dispersal prevails in the Central and South American species, a pattern not previously seen in plants.

The first phylogenetic analysis of Tetrastigma (Miq.) Planch., the host of Rafflesiaceae

AbstractTetrastigma (Vitaceae) comprises about 95 species widely distributed throughout subtropical and tropical Asia, and extending to Australia. The genus is best known for being the host plants of Rafflesia, with the largest flower in the world, and other members of Rafflesiaceae. The phylogeny of Tetrastigma, however, remains poorly known. Four plastid markers (atpB‐ rbcL, psbA‐trnH, trnL‐trnF intergenic spacers, rps16 intron) were employed to infer the first phylogeny of Tetrastigma. Our sampling included eleven reported host species of Rafflesiaceae, being scattered in seven major clades throughout the Tetrastigma tree. A Templeton test rejected the hypothesis of a single origin of the parasite‐host relationship between Rafflesiaceae and Tetrastigma. Analysis of 114 accessions representing 53 species and four varieties throughout the distributional range of the genus provided robust support for the monophyly of Tetrastigma, yet Tetrastigma was found to be nested within Cayratia. Tetrastigma subg. Palmicirrata from the Sino‐Himalayan region was nested within the large and widely distributed T. subg. Tetrastigma. Two major clades (clades A and F) in our phylogeny correspond to T. sect. Tetrastigma and T. sect. Carinata of subgenus Tetrastigma, respectively.

Molecular phylogenetics of moray eels (Muraenidae) demonstrates multiple origins of a shell-crushing jaw (Gymnomuraena, Echidna) and multiple colonizations of the Atlantic Ocean

Moray eels (Muraenidae) are apex predators on coral reefs around the world, but they are not well studied because their cryptic habitats and occasionally aggressive behaviors make them difficult to collect. We provide a molecular phylogeny of moray eels including 44 species representing two subfamilies, eight genera, and all tropical ocean basins. Phylogenetic relationships among these taxa are estimated from portions of mitochondrial loci cytochrome b (632bp) and cytochrome oxidase subunit 1 (596bp), and portions of the nuclear loci RAG-1 (421bp) and RAG-2 (754bp). We test four sets of contrasting phylogenetic hypotheses using Bayes Factors, Shimodaira–Hasegawa tests, and Templeton tests. First, our results support the subfamily-level taxonomic distinction between true morays (Muraeninae) and snakemorays (Uropterygiinae), statistically rejecting hypotheses of non-monophyly for each subfamily. Second, we reject a monophyletic grouping of the genera Gymnomuraena and Echidna, which share a durophagous (shell-crushing) cranial morphology and dentition, indicating that the durophagous characters are not homologous. Third, we demonstrate that durophagous feeding habits and associated morphological characters have evolved in parallel in an ancestor of Gymnomuraena and at least three additional times within the genus Echidna. Finally, the tree topology indicates multiple invasions of the Atlantic from the Indo-Pacific, one of these occurring immediately prior to formation of the Isthmus of Panama approximately 2.8MYA (million years ago) and one or two others occurring in the early to mid Miocene. Cladogenesis occurring within the Atlantic during the mid Miocene and Pliocene also contributed to moray species diversity. These data include a pair of sister species separated by the Isthmus of Panama, allowing a time-calibrated tree with an estimated crown age for Muraenidae at between 41 and 60MYA, consistent with fossil evidence. Most lineage accumulation within morays occurred from the late Oligocene (24–27MYA) through the Miocene (5–23MYA) to the late Pliocene (∼2.5MYA).

Combining Data from DNA Sequences and Morphology for a Phylogeny of Moringaceae (Brassicales)

Abstract The Old World dry tropical family Moringaceae is remarkable for the great diversity of habit and floral morphology found within its only genus, Moringa. To infer the phylogenetic relationships of all 13 species, parsimony analyses of morphological data and DNA sequences from a low-copy nuclear region (PEPC), a chloroplast region (trnG), and a tandemly-repeated nuclear region present in high copy number (ITS) were conducted of each data set separately and combined. Characters from studies of ontogeny substantially enhanced the resolution of the morphological data set. The Incongruence Length Difference test indicated the congruence of all data sets, as did Templeton tests comparing the single tree resulting from the combined analysis in the context of the individual data sets. This tree is presented as the preferred topology, in which the four bottle trees appear in a basal paraphyletic assemblage, with the three species of slender trees (including the economically important M. oleifera) forming a...

Molecular data do not support a southern hemisphere base of Nothofagus powdery mildews

Three powdery mildew species present on Nothofagus (viz. Erysiphe magellanica, E. nothofagi and E. patagoniaca) are endemic to South America and have unique ascomatal appendages that are not found in powdery mildews of the northern hemisphere. We determined the nucleotide sequences of the rDNA internal transcribed spacer regions and D1/D2 domains of the 28S rDNA of these three powdery mildew species to reveal their phylogenetic relationships with powdery mildews of the northern hemisphere. Although the molecular phylogenetic analyses indicated that the three Nothofagus powdery mildews are closely related to each other they did not group into one clade in either the ITS or 28S trees. Kishino-Hasegawa, Shimodaira-Hasegawa and Templeton tests could not significantly reject the constrained trees that were constructed based on the assumption that the Nothofagus powdery mildews would form a single clade. Based on this result and the evidence that all Nothofagus powdery mildews are endemic to South America and have similar morphological characteristics, it is likely that these three species diverged from a single ancestor present on Nothofagus. Calibration of evolutionary events with molecular clocks suggested that the Nothofagus powdery mildews split from the northern hemisphere relatives 22–16 million y ago (Ma) in the middle Miocene, and divergence among the Nothofagus powdery mildews occurred 17–13 Ma. These results do not support a southern hemisphere base of the Nothofagus powdery mildews.

Insights into the phylogenetic relationships within Cixiidae (Hemiptera: Fulgoromorpha): cladistic analysis of a morphological dataset

Abstract According to the most recent classifications proposed, the planthopper family Cixiidae comprises three subfamilies, namely Borystheninae, Bothriocerinae and Cixiinae, the latter with 16 tribes. Here we examine morphological characters to present the first phylogenetic reconstructions within Cixiidae derived from a cladistic analysis. We scored 85 characters of the head, thorax, and male and female genitalia for 50 taxa representative of all cixiid subfamilies and tribes and for six outgroup taxa. Analyses were based on maximum parsimony – using both equally weighted and successive weighting procedures – and Bayesian inferences. The monophyly of most currently accepted tribes and subfamilies was investigated through Templeton statistical tests of alternative phylogenetic hypotheses. The cladistic analyses recover the monophyly of Cixiidae, the subfamily Bothriocerinae, and the tribes Pentastirini, Mnemosynini, and Eucarpiini. Successive weighting and Bayesian inference recover the monophyly of the tribe Gelastocephalini, but only Bayesian inference supports the monophyly of Semoniini. The relationships recovered support the groups [Stenophlepsini (Borystheninae + Bothriocerinae)] arising from the tribe Oecleini, and [Andini + Brixiidini + Brixiini (polyphyletic) + Bennini]. Templeton tests reject the alternative hypothesis of a monophyletic condition for the tribe Pintaliini as presently defined.

A preliminary genetic distinctness of four Coilia fishes (Clupeiformes: Engraulidae) inferred from mitochondrial DNA sequences

In order to understand the genetic distinctness between four Coilia fishes,i.e., C. ectenes, C. e. taihuensis, C. mystus, and C. grayii, the combined cytochrome b (cytb), 12S rRNA and 16S rRNA gene sequences were obtained and analysed. The results are as follows: 1) neighbour-joining (NJ) and maximum parsimony (MP) trees were built with 1000 bootstrap replicates. They supported that Coilia fishes consisted of two clades: C. grayii form a monophyletic group, and the rest samples form the other monophyletic group; 2) the topological differences between the NJ tree and the MP tree are checked by Templeton test, indicating that their differences are insignificant (P > 0.05); and 3) Kimura-2-parameter distances between the samples of C. ectenes, C. e. taihuensis and C. mystus are all no bigger than 1.6%, and most of them are between 0.0% and 0.9%. C. ectenes, C. e. taihuensis and C. mystus are closely related and that their differences may be under subspecies.

Basal sauropodomorphs (Dinosauria: Saurischia) from the Lower Jurassic of India: their anatomy and relationships

The Upper Dharmaram Formation (Lower Jurassic, Sinemurian) of India has yielded three sauropodomorph dinosaurs, two new taxa and an indeterminate one.Lamplughsaura dharmaramensisn. gen. and sp., represented by several partial skeletons, is a heavily built quadrupedal form (body length ~10 m). Autapomorphies include teeth with strongly emarginated distal edge; caudal cervical neural spines bearing a vertically oriented ligamentous furrow on cranial and caudal surfaces and a transversely expanded spine table; caudal neural spines bearing a craniodorsally directed spur (proximal caudal vertebrae) or a large process (midcaudal vertebrae); caudal neural spines shorter than transverse processes so former lost first in passing along tail; and a plesiomorphy that is the nontrenchant form of manual ungual I. The Indian dinosaurs were coded for two recent datamatrices for basal sauropodomorphs. The results of this preliminary analysis indicate thatLamplughsaurais either a basal Sauropoda or, less likely, based on Templeton's test, a stem sauropodomorph. The second large form, represented by the proximal half of a femur, is a sauropodomorph that is more derived thanSaturnalia(Brazil) andThecodontosaurus(Great Britain) from the Upper Triassic. This is also true for the smaller (body length ~4 m as adult)Pradhania gracilisn. gen. and sp. which lies outside of the Sauropoda + Plateosauria clade, so it is definitely a stem sauropodomorph.Pradhaniais known from fragmentary material; an autapomorphy is the very prominent medial longitudinal ridge on the maxilla.

Multilocus phylogenetic analyses within Blumeria graminis, a powdery mildew fungus of cereals

Blumeria graminis, a powdery mildew fungus, is an important plant pathogen that causes serious damage to a variety of cereal crops. In spite of the importance of the pathogen, information on phylogenetic structure within B. graminis is scarce. In this study we conducted phylogenetic analyses of B. graminis based on the DNA sequences of four different DNA regions (ITS, 28S rDNA, chitin synthase 1, and β-tubulin). The analyses revealed that the protein-coding regions have higher amounts of phylogenetic signals than rDNA regions and are useful for phylogenetic analyses of B. graminis. The present phylogenetic analyses revealed nine distinct groups in the B. graminis isolates used in this study, a result which was commonly supported by all trees constructed from the four DNA regions. Isolates from a single host genus belonged to a single group except for isolates from Lolium and Bromus, in which the isolates were split into two and three groups, respectively. Isolates from Agropyron, Secale and Triticum formed a distinct clade ( Triticum clade) with identical or similar DNA sequences. The Hordeum clade was a sister of the Triticum clade, and Poa and Avena clades were distantly related to the Triticum and Hordeum clades. This phylogenetic relationship of B. graminis is well concordant with the level of reproductive isolation between formae speciales and also with phylogeny inferred from a cytological study. Shimodaira–Hasegawa and Templeton tests using sequences of four different DNA regions significantly rejected the tree topology of plants. Therefore, possibility of co-speciation between B. graminis and its host plants was obscure in this study.

A phylogenetic analysis of species in the Bufo crucifer group (Anura: Bufonidae), based on indolealkylamines and proteins from skin secretions

This research tested the utility of two classes of skin secretion compounds to the phylogeny of the Bufo crucifer group. Skin secretions from specimens of nine populations of B. crucifer group were obtained and submitted to qualitative analysis. We observed a clear difference in the composition of the skin secretion molecules obtained from the species of Bufo studied. Fifty-nine molecules, 16 indolealkylamines and 43 proteins, were used as characters, and 39 of these were parsimonious informative. The tree topology of the skin secretion combined data showed areas of congruence and conflict when compared to an mtDNA phylogeny of the B. crucifer group. We used the Templeton test to evaluate the heterogeneity between the skin secretion and mtDNA data. Although not recommended, we performed a combined analysis with the two partitions. The skin secretion characters from the species of Bufo studied have phylogenetic signal. These data are indicative, at least as a preliminary study, of the phylogenetic relationships among the B. crucifer group taxa.

The complete mitochondrial genome of Anisakis simplex (Ascaridida: Nematoda) and phylogenetic implications

We determined the nucleotide sequence of the complete mitochondrial genome of the nematode species Anisakis simplex. The genome is circular, 13,916 bp in size and conforms to the general characteristics of nematode mitochondrial DNAs. The gene arrangement of A. simplex is the same as that of Ascaris suum and almost identical to those of rhabditid species with a minor exception concerning the relative position of the AT-rich and non-coding regions and radically different from those of spirurid species. Along with comparisons of gene arrangement, phylogenetic analyses (maximum parsimony, neighbour joining and maximum likelihood methods) based on concatenated amino acid sequences of 12 protein-coding genes from 13 nematode species provided strong support for the sister-group relationship between Ascaridida and Rhabditida. The Shimodaira–Hasegawa and Templeton's tests both rejected the alternative hypothesis of a closer relationship between Ascaridida and Spirurida. These results contradicted the traditional view of nematode classification and a recent molecular phylogenetic study of 18S rDNA data that assigned Ascaridida and Spirurida as being a sister-group. Mapping of gene arrangement across the phylogenetic tree lead to the assumption that the conserved gene arrangement found in Ascaridida–Rhabditida members might have been acquired after the most recent common ancestor of ascaridid/rhabditid members branched off from the basal stock of the rhabditid lineage.

The osteology and phylogeny of the Hawaiian finch radiation (Fringillidae: Drepanidini), including extinct taxa

The monophyly and phylogeny of the adaptive radiation of Hawaiian finches (Fringillidae: Drepanidini; honeycreepers, auct.) were studied using parsimony analysis of comparative osteology, combined with Templeton (Wilcoxon signed-ranks) tests of alternative phylogenetic hypotheses. Eighty-four osteological characters were scored in 59 terminal taxa of drepanidines, including 24 fossil forms, and in 30 outgroup species. The optimal phylogenetic trees show considerable agreement, and some conflict, with independently derived ideas about drepanidine evolution. The monophyly of a large Hawaiian radiation was upheld, although one fossil taxon from Maui fell outside the drepanidine clade. The finch-billed species were placed as basal drepanidine taxa, and continental cardueline finches (Carduelini) were identified as the radiation’s closest outgroups. The study found anatomical as well as phylogenetic evidence that the radiation had a finch-billed ancestor. The optimal trees identify the red-and-black plumage group as a clade, and suggest that the tubular tongue evolved only once in the radiation. Because comparative osteology provides too few characters to strongly support all the nodes of the tree, it was helpful to evaluate statistical support for alternative hypotheses about drepanidine relationships using the Templeton test. Among the alternatives that received significant statistical support are a relationship of the drepanidines with cardueline finches rather than with the Neotropical honeycreepers (Thraupini), classification of the controversial genera Paroreomyza and Melamprosops as drepanidines, and a secondary loss of the tubular tongue in Loxops mana. The hypothesis of monophyly for all the Hawaiian taxa in the study was not rejected statistically. The study provides a framework for incorporating morphological and palaeontological information in evolutionary studies of the Drepanidini. © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society, 2004, 141, 207‐255. ADDITIONAL KEYWORDS: adaptive radiation ‐ comparative anatomy ‐ evolution ‐ fossils ‐ Hawaiian honeycreepers ‐ island biogeography ‐ morphology ‐ palaeontology ‐ Passeriformes.

Phylogenetic analyses of the Lyophylleae (Agaricales, Basidiomycota) based on nuclear and mitochondrial rDNA sequences

Current classifications of the Lyophylleae and the importance of siderophilous granulation in the basidia for the classification of agaricoid fungi were evaluated using parsimony analyses of sequence data from the nuclear ribosomal large subunit gene (nLSU), the internal transcribed spacer region of the nuclear ribosomal array (ITS), and the mitochondrial ribosomal small subunit gene (mtSSU). These three different data partitions were phylogenetically congruent on the basis of the Mickevich-Farris statistical test, but not from the ILD and the Templeton tests. Bootstrap supports for nodes in phylogenetic trees generated from combined nLSU, ITS, and mtSSU sequence data were generally higher than those in trees generated from individual data sets. This suggests a lack of major conflict in the phylogenetic signal among the different data sets. We conclude that the Mickevich-Farris test is more appropriate for estimating congruence and combinability between different sources of molecular data than the more widely used ILD and Templeton tests, at least when the different data sets have their respective resolution power at different depths in the phylogeny. Results of the combined analyses show that the Entolomataceae are a sister group to a clade composed of the Lyophylleae, Termitomyceteae, and Tricholomateae p.p. This implies that presence of siderophilous granulation in the basidia of agaric fungi has probably a single origin, and would have been lost in the Tricholomateae. Inclusion of the Termitomyceteae within the Lyophylleae suggests homology of the macro type granulation. Because the exact placement of Tricholomateae pro parte remains uncertain, it remains unclear whether the Lyophylleae (including Termitomyceteae) are monophyletic or paraphyletic. Within the Lyophylleae, genera Lyophyllum and Calocybe are shown to be artificial, as are Lyophyllum sections Lyophyllum, Difformia, and Tephrophana. Four main natural groups of Lyophylleae have been identified that should serve as a basis for developing a more natural classification system for these fungi.

Paraphyletic Syringa (Oleaceae): Evidence from Sequences of Nuclear Ribosomal DNA ITS and ETS Regions

Sequences of nuclear ribosomal DNA ITS and ETS regions were used to examine phylogenetic relationships of Syringa and Ligustrum. Twenty-seven samples were included in parsimony analyses, representing all major groups of these two genera. Two species of Fraxinus and one species of Jasminum were also included in analyses for rooting purposes. In the resulting phylogenetic hypothesis series Syringa (Syringa) diverges first and is followed by the monotypic series Pinnatifoliae (Syringa), which is sister to a clade containing the remaining species of Syringa and species of Ligustrum. However, this sister relationship is weakly supported. Our results support the recognition of monophyletic groups corresponding to subgenus Ligustrina, and series Syringa, Pubescentes ,a ndVillosae, and suggest that Ligustrum as a monophyletic group is derived from within Syringa, such that Syringa as traditionally circumscribed is paraphyletic. Forcing Syringa to be mono- phyletic entails nine extra steps, which is significant, as judged by the Templeton test. Parasyringa sempervirens is phyloge- netically embedded within the Ligustrum clade, supporting its placement in Ligustrum. Berries are a synapomorphy of Ligustrum species, and the dehiscent berry of Parasyringa sempervirens is likely to be an evolutionary reversal towards a capsule, which is characteristic of Syringa. The evolution of berries might have contributed to an accelerated rate of speciation in Ligustrum.

Phylogenetic relationships of the Rhizophoraceae in China based on sequences of the chloroplast gene matK and the internal transcribed spacer regions of nuclear ribosomal DNA and combined data set

Abstract The chloroplast gene matK and the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA were sequenced from 17 samples of 13 species representing 6 genera of the angiosperm family Rhizophoraceae from China. Phylogenetic analyses were initially conducted based on sequences of the matK gene and the ITS regions, respectively, using Byrsonima crassifolia and Bunchosia armeniaca (Malpighiaceae) as outgroups. The partition–homogeneity test indicated that the two data sets are homogeneous. A combined analysis of the matK and ITS data generated a well supported phylogeny, which is topologically congruent with the two gene trees based on the Templeton test. The combined phylogeny shows that each genus formed a monophyletic group and the monophyletic relationships of the mangrove genera and of the inland genera were strongly supported.

Evolution of Fusarium oxysporum f. sp. vasinfectum Races Inferred from Multigene Genealogies

ABSTRACT Fusarium wilt of cotton is a serious fungal disease responsible for significant yield losses throughout the world. Evolution of the causal organism Fusarium oxysporum f. sp. vasinfectum, including the eight races described for this specialized form, was studied using multigene genealogies. Partial sequences of translation elongation factor (EF-1alpha), nitrate reductase (NIR), phosphate permase (PHO), and the mitochondrial small subunit (mtSSU) rDNA were sequenced in 28 isolates of F. oxysporum f. sp. vasinfectum selected to represent the global genetic diversity of this forma specialis. Results of a Wilcoxon Signed-Ranks Templeton test indicated that sequences of the four genes could be combined. In addition, using combined data from EF-1alpha and mtSSU rDNA, the phylogenetic origin of F. oxysporum f. sp. vasinfectum within the F. oxysporum complex was evaluated by the Kishino-Hasegawa likelihood test. Results of this test indicated the eight races of F. oxysporum f. sp. vasinfectum appeared to be nonmonophyletic, having at least two independent, or polyphyletic, evolutionary origins. Races 3 and 5 formed a strongly supported clade separate from the other six races. The combined EF-1alpha, NIR, PHO, and mtSSU rDNA sequence data from the 28 isolates of F. oxysporum f. sp. vasinfectum recovered four lineages that correlated with differences in virulence and geographic origin: lineage I contained race 3, mostly from Egypt, and race 5 from Sudan; lineage II contained races 1, 2, and 6 from North and South America and Africa; lineage III contained race 8 from China; and lineage IV contained isolates of races 4 and 7 from India and China, respectively.

Phylogenetic structure of the genus Leveillula (Erysiphales: Erysiphaceae) inferred from the nucleotide sequences of the rDNA ITS region with special reference to the L. taurica species complex

The nucleotide sequences of the nuclear ribosomal DNA, including ITS1, ITS2 and the 5.8S rDNA, were determined for 54 specimens representing 13 Leveillula species on 50 different host plant species. The maximum nucleotide sequence diversity among taxa in ITS1-5.8S-ITS2 was 7.1%. Phylogenetic analyses revealed that Leveillula species formed six clades and three basal taxa. The taxonomic positions of several species that are well characterized by morphology of conidia, especially primary conidia, are supported by the present molecular analyses. This result shows that the morphology of primary conidia mostly provides a good criterion to identify Leveillula species. Twenty-six collections of Leveillula taurica recovered from 14 different plant families formed a distinct clade with L. chrozophorae, L. duriaei and L. elaeagni, and showed high homology in the ITS regions. Eight isolates of L. taurica recovered from the Asteraceae, Balsaminaceae, Fabaceae and Campanulaceae showed high sequence diversity, in contrast with other L. taurica specimens, and clustered separately or with other taxa. The result of Kishino-Hasegawa and Templeton tests demonstrated that the possibility of monophyly of L. taurica s. lat. could be significantly rejected, indicating that L. taurica s. lat. is a species complex composed of several biological species.