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.     

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.

     

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.     

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.     

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 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.     

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     

Cladistic analysis of Taxaceae s. l.

Taxaceae s. l. is a wider concept of classification treating five genera of Taxaceae s. str. and Cephalotaxus together. Cephalotaxus is morphologically very similar to the five genera of Taxaceae s. str. Various models of classification for six genera have already been published. However, the phylogenetic position and genuine relationships of these genera and species are still confusing. A cladistic analysis of Taxaceae s. l. has been carried out to resolve the problem existing in their phylogeny and to provide a new approach regarding the relationships of these six genera. Parsimony analyses were based on 28 characters and eight genera including two outgroups Agathis and Sciadopitys. The most parsimonious tree retained with branch length 38 and 194 rearrangement trials. Consistency index was 0.68 and retention index was 0.66. Principally, two main clades were found: one represented by Austrotaxus forming the base of the tree and another by the remaining five genera. Taxus + Pseudotaxus clade split after Austrotaxus, and Cephalotaxus was sister to Torreya + Amentotaxus clade. Taxus + Pseudotaxus clade was supported by the highest bootstrap value. Finally, cladistic analysis does not support existence of Cephalotaxaceae. Therefore, it would be better to classify Cephalotaxus within Taxaceae s. l. with the other five genera.     

A revision of Clematis sect. Aspidanthera s.l. （ Ranunculaceae ）

对毛茛科铁线莲属Clematis L.的单性铁线莲组sect. Aspidanthera Spach s.l.进行了全面修订,确定此组共含72种和15变种,这些种被归类于6个亚组中,其中包括首次描述的1系、5种和2变种,以及做出的2新等级.对单性铁线莲组的分类学简史和地理分布做了介绍.写出了组、亚组、系的形态特征和地理分布,分亚组检索表及各亚组的分种检索表;以及各种植物的形态描述、地理分布、生长环境等,并附有多幅插图.在研究了此组全部种类的标本之后,观察到此组几个重要形态特征的演化趋势(1)萼片在数目上由4枚演变到8枚,在开展方向上由平展到直上展,在形状上由长圆形到狭条形,在长度上由比雄蕊稍长到2-4倍长于雄蕊,其卷叠式由镊合状到次生的覆瓦状;(2)花药药隔顶端由不具突起到具短或长的突起;(3)雌花退化雄蕊的数目由多数到定数、少数,以至完全消失;(4)花序自当年生枝的叶腋发生演变到与数叶同自老枝的一腋芽中发出.根据上述演化趋势推断本组各亚组间的亲缘关系如下subsect. Dioicae (34种,广布于北美洲和南美洲)的花构造(萼片4,镊合状排列,平展,通常呈长圆形,稍长于雄蕊或近等长,外面边缘被短绒毛;雄蕊花药呈长圆形,药隔顶端无突起;雌花具多数退化雄蕊;花序自当年生枝的叶腋发出)与具两性花的威灵仙组欧洲铁线莲亚组sect. Clematis subsect. Clematis 的花极为相似,区别主要在于本亚组的花为单性,由此判断subsect. Dioicae可能是单性铁线莲组sect. Aspidanthera的原始群,源出于欧洲铁线莲亚组.本组的第二亚组subsect. Lasianthae(2种,分布于北美西南部)与subsect. Dioicae 在亲缘关系上极为相近,区别只在于其花序或具花当年生枝与数叶一同由老枝的一个腋芽中发出,此亚组当是从subsect. Dioicae衍生出的一个小群.第三亚组subsect. Microphyllae(7种,特产澳大利亚)也与subsect. Dioicae相近缘,但此亚组的萼片变狭长,多呈条形或狭条形,常2-4倍长于多少变短的雄蕊,雌花的退化雄蕊数目变少,16-2枚,根据这些进化特征,推测此亚组也源出于subsect. Dioicae.第四亚组subsect. Aristatae (16种,分布于澳大利亚、新几内亚及邻近岛屿)与subsect. Microphyllae 在亲缘关系上相近,但本亚组的花药药隔顶端具短或长的突起而不同,根据此进化特征,推测本亚组系由后者演化而出.第五亚组subsect. Hexapetalae (11种,特产新西兰)的花构造与分布于澳大利亚的subsect. Microphyllae相似,但其萼片为覆瓦状排列,外面边缘不被短绒毛,在多数种多于4枚,为5-8枚而不同.据Godley 的研究,本亚组中的C. afoliata的花有4枚萼片,排成2轮,每轮的2枚萼片均为近镊合状排列;另外,在C. paniculata花的6枚萼片中,4枚为覆瓦状排列,其他2枚有时内向镊合状排列.从上述情况可见此亚组的萼片覆瓦状卷叠式可能是由镊合状卷叠式演变而来的一种次生现象,并由此推测,此亚组可能与subsect. Microphyllae相同,也源自美洲的subsect.Dioicae.最后一个亚组subsect. Insidiosae(2种,特产马达加斯加)的雌花萼片直上展,退化雄蕊完全消失,具有这些进化特征,当是单性铁线莲组的进化群,可能源出自具定数或少数退化雄蕊的subsect. Microphyllae.     

Isolation of Klebsielleae from within living wood.

Previous studies from this laboratory have documented the presence of coliform bacteria emanating from wooden reservoirs containing finished drinking water. Coliforms were identified as Klebsiella pneumoniae and Enterobacter spp. In the present report, evidence is presented which suggests that the origin of these coliforms is from the wood used to construct the reservoirs. In liquid expressed from freshly cut redwood, total bacterial counts in the range of 10(5) to 10(6)/ml were commonly observed. When present, coliform counts were over 10(3)/ml of expressed liquid. E. agglomerans was the most prevalent coliform present, but Klebsiella was isolated from freshly cut logs. Citrobacter freundii was also occasionally isolated. No fecal coliform-positive Klebsiella were obtained from any of the samples. Highest total bacteria and coliform counts were observed in sapwood specimens. Coliforms were present throughout sapwood as evidenced by contact plating serial sections of freshly cut wood. Scanning electron micrographs illustrate the presence of bacterial colonies within sapwood tracheids. Other wood species also contained coliform bacteria but in numbers lower than found in redwood.     

A chemometric comparison of three taxa of Scabiosa L.s.l.

ABSTRACT

A comparative chemometric study of three taxa of the genus Scabiosa L. s. lato (Dipsacaceae) from Greece, treated so far as separate genera by some authors and as separate sections of a single genus by others, was carried out. The HPLC chemical fingerprint, based on several phenolic compounds (flavonoids and caffeic acid), was investigated in the three a forementioned taxa. The results support the contention that there is a close relationship between S. atropurpurea subsp. maritima and S. tenuis, and that S. argentea seems to be well separated from the other two taxa.     

Ultrastructural features of the tegumental surface of a new metacercaria, Nematostrigea sp. (Trematoda: Strigeidae), with a search for potential taxonomically informative characters

The tegumental surface of a new strigeid metacercaria, Nematostrigea sp., which is a parasite of the freshwater fish Channa gachua (Hamilton) in central Vietnam, is described for the first time using scanning (SEM) and transmission (TEM) electron microscopy. In addition to the general tegumental surface in various parts of the body, details of the surface of the suckers, lappets and holdfast organ are presented, as are variations in the form and distribution of the body spines. As good taxonomic criteria are few in diplostomoid metacercariae at both specific and generic levels, a number of the ultrastructural features revealed may prove to represent taxonomically informative characters. These include the presence of: two rings of dome-shaped papillae localised at different levels on the rim of the oral sucker, a single ring of ciliated papillae on the inner margin of the ventral sucker and a band of dome-shaped papillae along the lateral margins of the broad body-fold in the ventral forebody; an unarmed oral sucker and anteroventral surface of the forebody, although the latter bears protuberant secretory pores; an armed ventral sucker covered by six-pointed spines, except on its rim; multi-pointed spines along the dorsal and ventral sides of the forebody, with the number of their teeth increasing posteriorly; multi-pointed spines on the forebody which gradually transform into single-pointed, more widely distributed spines on the hindbody, disappearing completely at posterior end of the body; the surface of the lappets with a particular distribution of pores leading to three types of secretory glands and three topographical modifications (areas where the surface is smooth, bears digitiform processes or bears recurved, dagger-shaped spines); and the surface of the holdfast organ which is covered with densely packed, straight or slightly curved, simple spines on its lateral surface but is smooth medially.     

Androecial development and systematics inFlacourtiaceae s. l.

Androecial development of 13 species belonging to six tribes ofFlacourtiaceae has been investigated. While inScolopieae andFlacourtieae the stamens develop centrifugally, inErythrospermeae, Oncobeae andPangieae they are initiated in a centripetal sequence or a sequence that is neither distinctly centripetal nor centrifugal. The distribution of these developmental patterns coincides with the distribution of other characters (e.g. cyanogenic compounds, salicoid leaf teeth) and therefore supports a split of the family intoFlacourtiaceae s. str. (containing theScolopieae, Homalieae, Prockieae, Flacourtieae, Casearieae andBembicieae) andKiggelariaceae (withErythrospermeae, Oncobeae andPangieae) and is in accordance with results of recentrbcL studies.