DNA sequence polymorphism within hominoid species exceeds the number of phylogenetically informative characters for a HOX2 locus.

Within- and between-species variability was examined in a noncoding 238-bp segment of the HOX2 cluster. DNA of 4-26 individuals of four species (Pongo pygmaeus, Pan troglodytes, Gorilla gorilla, and Homo sapiens) was PCR amplified and electrophoresed in a denaturing gradient gel to screen for variability. Coupled amplification and sequencing was used to determine the complete sequence for each of the different alleles identified, one each in humans and orangutans, two in chimpanzees, and four in gorillas. Maximum-parsimony methods were used to construct a gene tree for these sequences. Alleles in all four species cluster into groups consisting of only one species (i.e., alleles within a species are monophyletic). The number of base-pair differences observed among alleles within P. troglodytes and within G. gorilla is larger than the number of base-pair substitutions that phylogenetically link Pan with Homo. Given these and other published data, it is premature to accept any particular phylogenetic tree that relates these three genera through two separate speciation events.     

A PCR-based method for the identification of important wood rotting fungal taxa within Ganoderma, Inonotus s.l. and Phellinus s.l

Two multiplex PCRs, based on 10 taxon-specific primers designed on rRNA gene regions, were developed for the identification of taxa within the lignivorous genera Ganoderma, Inonotus s.l. and Phellinus s.l., each comprising both secondary and primary aggressive decay fungi. Each multiplex PCR proved to correctly identify 1 x 10(-2) pg of fungal target DNA directly from wood. This method can be helpful in detecting decay in standing trees independent of its stage of advancement, and to identify the associated decay agents.     

Efficient enumeration of phylogenetically informative substrings.

We study the problem of enumerating substrings that are common amongst genomes that share evolutionary descent. For example, one might want to enumerate all identical (therefore conserved) substrings that are shared between all mammals and not found in non-mammals. Such collection of substrings may be used to identify conserved subsequences or to construct sets of identifying substrings for branches of a phylogenetic tree. For two disjoint sets of genomes on a phylogenetic tree, a substring is called a tag if it is found in all of the genomes of one set and none of the genomes of the other set. We present a near-linear time algorithm that finds all tags in a given phylogeny; and a sublinear space algorithm (at the expense of running time) that is more suited for very large data sets. Under a stochastic model of evolution, we show that a simple process of tag-generation essentially captures all possible ways of generating tags. We use this insight to develop a faster tag discovery algorithm with a small chance of error. However, since tags are not guaranteed to exist in a given data set, we generalize the notion of a tag from a single substring to a set of substrings. We present a linear programming-based approach for finding approximate generalized tag sets. Finally, we use our tag enumeration algorithm to analyze a phylogeny containing 57 whole microbial genomes. We find tags for all nodes in the phylogeny except the root for which we find generalized tag sets.     

Fasciole pathways in spatangoid echinoids: a new source of phylogenetically informative characters

Fascioles are important early-forming structures that play a key role in allowing irregular echinoids to burrow. They have traditionally been grouped into a small number of types according to their general position on the test, but this masks some significant differences that exist. The precise course that fasciole bands follow over the test plating has been mapped in detail for 89 species of spatangoid echinoids, representing the great majority of fasciole-bearing genera both living and fossil. Within each fasciole type, discrete and conserved patterns can be distinguished, differing both in which plates they are initiated on, and on whether they cross plate growth centres or are late-stage bands positioned towards the edge of the plate. Fasciole position is most highly conserved in the anterior and lateral interambulacral plates and on the earliest forming bands. The existence of different subanal fasciole patterns in the Micrasteridae and Brissidae suggests that these may have evolved independently. Schizasterid and hemiasterine spatangoids can each be subdivided into two major clades, and brissid spatangoids into three clades based on detailed patterns of their fascioles. Plotting fasciole pathways over test architecture provides a rich new source of phylogenetically informative characters.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 144 , 15−35.     

Trichome morphology provides phylogenetically informative characters for Tremandra, Platytheca and Tetratheca (former Tremandraceae)

Summary Trichomes of Tremandra R.Br. ex DC., Platytheca Steetz and Tetratheca Sm. (Elaeocarpaceae, former Tremandraceae), together with two outgroup species of Elaeocarpus L., are illustrated using scanning electron microscopy, and their distribution on various plant organs is documented. Various trichomes types were identified that relate taxa: simple hairs, stellate hairs, short glandular trichomes, long glandular trichomes, and three forms of tubercules. Both outgroup and ingroup taxa have simple hairs. Stellate hairs are confirmed as unique to Tremandra. Prominent and sculptured multicelled tubercules, some bearing a stout hair, are characteristic of Platytheca. Smaller multicelled tubercules occur in both Platytheca and Tetratheca, except for the Western Australian taxon Te. filiformis Benth. (possibly plesiomorphic). Unicellular tubercules (papilla) characterise two species of Tetratheca. Short glandular trichomes, usually found on the ovary, also occur in both of these genera but not in all species (possibly secondary losses), while long glandular trichomes, usually on stems and leaves, occur only in some groups of Tetratheca. Within Tetratheca, Western Australian taxa that have five-merous flowers fall into three ‘groups’: seven species (together with one from South Australia) that have short glandular trichomes but no long glandular trichomes; six species that have long glandular trichomes but no short glandular trichomes; and four species that have both trichome types. All other species of Tetratheca have four-merous flowers and form two ‘groups’: 12 eastern species (including one from South Australia) that have both short glandular trichomes and long glandular trichomes; 4 western species and six eastern species that lack short glandular trichomes. On the basis of these characters, a phylogenetic hypothesis for the three genera is presented.     

Automated scanning for phylogenetically informative transposed elements in rodents

Transposed elements constitute an attractive, useful source of phylogenetic markers to elucidate the evolutionary history of their hosts. Frequent and successive amplifications over evolutionary time are important requirements for utilizing their presence or absence as landmarks of evolution. Although transposed elements are well distributed in rodent taxa, the generally high degree of genomic sequence divergence among species complicates our access to presence/absence data. With this in mind we developed a novel, high-throughput computational strategy, called CPAL (Conserved Presence/Absence Locus-finder), to identify genome-wide distributed, phylogenetically informative transposed elements flanked by highly conserved regions. From a total of 232 extracted chromosomal mouse loci we randomly selected 14 of these plus 2 others from previous test screens and attempted to amplify them via PCR in representative rodent species. All loci were amplifiable and ultimately contributed 31 phylogenetically informative markers distributed throughout the major groups of Rodentia.     

A composite genome approach to identify phylogenetically informative data from next-generation sequencing

Background

Improvements in sequencing technology now allow easy acquisition of large datasets; however, analyzing these data for phylogenetics can be challenging. We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps of de novo whole genome assembly, multiple genome alignment, and annotation.

Results

For simulations SISRS is able to identify large numbers of loci containing variable sites with phylogenetic signal. For genomic data from apes, SISRS identified thousands of variable sites, from which we produced an accurate phylogeny. Finally, we used SISRS to identify phylogenetic markers that we used to estimate the phylogeny of placental mammals. We recovered eight phylogenies that resolved the basal relationships among mammals using datasets with different levels of missing data. The three alternate resolutions of the basal relationships are consistent with the major hypotheses for the relationships among mammals, all of which have been supported previously by different molecular datasets.

Conclusions

SISRS has the potential to transform phylogenetic research. This method eliminates the need for expensive marker development in many studies by using whole genome shotgun sequence data directly. SISRS is open source and freely available at https://github.com/rachelss/SISRS/releases.

     

Latitudinal trends in wood anatomy within species and genera: case study in Cornus s.l. (Cornaceae)

Latitudinal trends in wood anatomical characters in three Asiatic species of Cornus sensu lato (s.l.) were studied and compared with those for the whole genus based on an extensive sampling covering the specific distribution ranges and the generic data from a previous study. We studied 124 specimens of C. controversa growing between 31.5° and 45.3° N, 54 of C. kousa between 24.4° and 40.5° N, and 64 of C. macrophylla between 27.8° and 41.0° N. Characters studied were vessel element length, fiber length, vessel frequency, tangential vessel diameter, and vessel grouping index. At the species level no latitudinal trends were detected throughout the distribution ranges of the species. Neither tree size, altitude, nor climatic factors had a significant correlation with wood anatomical characters. In contrast, at the genus level, latitudinal trends were significant not just for the whole genus, but for both New and Old World species groups. At the genus level, latitude and three climatic factors all had a significant correlation with wood anatomical characters, but correlation coefficients with latitude were markedly high. The difference in latitudinal trends between the genus and species levels may be due to the radiation of Cornus along paleoclimatic gradients in the early Tertiary.     

Wood and bark anatomy of Muntingiaceae: A phylogenetic comparison within Malvales s. l.

Quantitative and qualitative data on wood and bark anatomy are given for Muntingia calabura L. and Dicraspidia donnell-smithii Standley. These data are compared with phylogenetic schemes, based on DNA analysis, in which Muntingiaceae belong to the “dipterocarp clade” within Malvales. The data are consistent with this hypothesis, although Muntingiaceae lack pit vestures in vessels, which are seen in the other malvalean families (Cistaceae, Dipterocarpaceae, Neuradaceae, Sarcolaenaceae, Thymeleaceae), and this may represent a loss of pit vestures. All families of the dipterocarp clade agree with both genera of Muntingiaceae in having tracheids as the imperforate tracheary element type (at least ancestrally), although fiber-tracheids also occur in some Dipterocarpaceae and Thymeleaceae. The large size of some malvalean families (with attendant greater diversity in character states) and a paucity of wood studies in those families make for difficulty in comparison of features such as axial parenchyma and ray types with those of Muntingiaceae; character states of these features are consistent with placement of Muntingiaceae in the dipterocarp clade of Malvales. Banded phloem fibers in bark of Muntingiaceae are much like those of other Malvales. Wood of Muntingiaceae is highly mesomorphic according to quantitative vessel features.     

A multiplex bead-based suspension array assay for interrogation of phylogenetically informative single nucleotide polymorphisms for Bacillus anthracis

Single nucleotide polymorphisms (SNPs) are abundant in genomes of all species and represent informative DNA markers extensively used to analyze phylogenetic relationships between strains. Medium to high throughput, open methodologies able to test many SNPs in a minimum time are therefore in great need. By using the versatile Luminex® xTAG technology, we developed an efficient multiplexed SNP genotyping assay to score 13 phylogenetically informative SNPs within the genome of Bacillus anthracis. The Multiplex Oligonucleotide Ligation-PCR procedure (MOL-PCR) described by Deshpande et al., 2010 has been modified and adapted for simultaneous interrogation of 13 biallelic canonical SNPs in a 13-plex assay. Changes made to the originally published method include the design of allele-specific dual-priming-oligonucleotides (DPOs) as competing detection probes (MOLigo probes) and use of asymmetric PCR reaction for signal amplification and labeling of ligation products carrying SNP targets. These innovations significantly reduce cross-reactivity observed when initial MOLigo probes were used and enhance hybridization efficiency onto the microsphere array, respectively. When evaluated on 73 representative samples, the 13-plex assay yielded unambiguous SNP calls and lineage affiliation. Assay limit of detection was determined to be 2 ng of genomic DNA. The reproducibility, robustness and easy-of-use of the present method were validated by a small-scale proficiency testing performed between four European laboratories. While cost-effective compared to other singleplex methods, the present MOL-PCR method offers a high degree of flexibility and scalability. It can easily accommodate newly identified SNPs to increase resolving power to the canSNP typing of B. anthracis.     

Comparative wood anatomy of Andromedeae s.s., Gaultherieae, Lyonieae and Oxydendreae (Vaccinioideae, Ericaceae s.l.)

The wood anatomical structure of 11 out of 13 genera from four tribes of the Vaccinioideae, namely Andromedeae s.s. , Gaultherieae, Lyonieae and Oxydendreae (Ericaceae s.l. ), is described using light and scanning electron microscopy. Several features of the secondary xylem support the tribal classification based on molecular data: arrangement of vessel-ray pitting, height of multiseriate rays and the shape of the body ray cells. Oxydendreae are clearly defined from the other representatives by various wood anatomical features. Gaultherieae can be distinguished from Lyonieae by differences in vessel perforation plates, vessel-ray pitting, height and structure of multiseriate rays, and occurrence of prismatic crystals, but the wood of Andromedeae s.s. is similar to Gaultherieae. Moreover, Andromedeae s.s. , Oxydendreae and Vaccinieae are characterized by their pith structure, whereas considerable variation in the pith cells is found in Lyonieae and Gaultherieae.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 144 , 161–179.     

A phylogenetically conserved sequence within viral 3'' untranslated RNA pseudoknots regulates translation.

Both the 68-base 5' leader (omega) and the 205-base 3' untranslated region (UTR) of tobacco mosaic virus (TMV) promote efficient translation. A 35-base region within omega is necessary and sufficient for the regulation. Within the 3' UTR, a 52-base region, composed of two RNA pseudoknots, is required for regulation. These pseudoknots are phylogenetically conserved among seven viruses from two different viral groups and one satellite virus. The pseudoknots contained significant conservation at the secondary and tertiary levels and at several positions at the primary sequence level. Mutational analysis of the sequences determined that the primary sequence in several conserved positions, particularly within the third pseudoknot, was essential for function. The higher-order structure of the pseudoknots was also required. Both the leader and the pseudoknot region were specifically recognized by, and competed for, the same proteins in extracts made from carrot cell suspension cells and wheat germ. Binding of the proteins is much stronger to omega than the pseudoknot region. Synergism was observed between the TMV 3' UTR and the cap and to a lesser extent between omega and the 3' UTR. The functional synergism and the protein binding data suggest that the cap, TMV 5' leader, and 3' UTR interact to establish an efficient level of translation.     

中国广义杯伞属真菌名称（英文）

对广义杯伞属(Clitocybe s.l.)分类研究现状的调查结果表明,我国已报道的广义杯伞属共有110个种及种下分类单元,其中72个名称的报道具有标本引证、51个名称为其他分类单元的异名或已组合至其他属中、2个名称为其他属分类单元的笔误。亚白杯伞(Clitocybe subcandicans Z.S.Bi)为国外先发表的C.subcandicans Murrill.的晚出同名。此外,与国外文献的描述相比,国内报道的一些广义杯伞属种类存在明显的形态差异。     

A revised classification of the Apocynaceae s.l.

The Asclepiadaceae, as traditionally defined, have repeatedly been shown to be an apomorphic derivative of the Apocynaceae. It has often been recommended that the Asclepiadaceae be subsumed within the Apocynaceae in order to make the latter monophyletic. To date, however, no comprehensive, unified classification has been established. Here we provide a unified classification for the Apocynaceae, which consists of 424 genera distributed among five subfamilies: Rauvolfioideae, Apocynoideae, Periplocoideae, Secamonoideae, and Asclepiadoideae. Keys to the subfamilies and tribes are provided, with lists of genera that (as far as we have been able to ascertain) are recognized in each tribe.     

Multivariate analyses of morphological characters of Leptolaena Thouars s.l. subgenera Mediusella and Xerochlamys (Sarcolaenaceae)

Leptolaena Thouars is one of the first described genera within Sarcolaenaceae, but represents the last great species-level taxonomic challenge in this endemic Malagasy plant family. As currently circumscribed, this genus comprises three subgenera, two of which, Mediusella Cavaco and Xerochlamys (Baker) Cavaco, exhibit patterns of morphological variation that have been understood differently and have led to an unstable taxonomy, such that a consensus on the delimitation of species has yet to be reached. Principal component analysis of morphological characters was performed on 211 herbarium specimens in order to evaluate the morphological variation within the two subgenera and to clarify historically problematical species boundaries. The results showed that ten entities could be distinguished on the basis of vegetative, floral, and fruit characters, and that they provide a robust basis for proposing a new species-level taxonomic framework.  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 157 , 559–574.     

Thlaspi s.str. (Brassicaceae) versus Thlaspi s.l.: morphological and anatomical characters in the light of ITS nrDNA sequence data

 Nuclear ribosomal (ITS) DNA sequence data from representatives of eleven out of 12 genera previously included in Thlaspi sensu lato were analyzed to elucidate relationships within the former genus Thlaspi sensu lato. Sequences from Thlaspi segregates Noccaea, Masmenia, Callothlaspi, Kotschyella, Microthlaspi, and Noccidium were added to the existing data sets, and only some Thlaspi sensu lato segregates formed a monophyletic group. The recently renamed genus Pseudosempervivum, formerly part of the genus Cochlearia, has been shown to be closely related to this group as well. Microthlaspi consists of three independent lineages of which Microthlaspi umbellatum is closely related to Neurotropis. The Thlaspi s.str. taxa including the type species T. arvense, are closely related to Peltaria and Alliaria and they represent a monophyletic group. Kotschyella and Noccidium, which were also integrated into Thlaspi s.l. are not closely related to any Thlaspi lineage. Therefore, we suggest major taxonomical changes which are not in agreement with concepts based on morphological data. Our ITS based phylogeny demonstrates that subtribe Thlaspidinae comprises some additional genera such as Teesdalia, Peltaria, and Alliaria, the latter two even previously classified in other tribes than tribe Lepidieae. Received August 15, 2000 Accepted January 30, 2001