COMMENTS ON GENOMIC GENERA IN THE TRITICEAE (POACEAE)

Generic delimitation in the Triticeae has long been problematical because the extensive hybridization in the group is not readily accomodated in a hierarchical classification. The genomic genera of Löve (1984) are one solution, but fully one-third of them are polyphyletic, incorporating 2 or more genomes. The suggestion that the tribe be considered a single genus (Stebbins, 1956) is theoretically defensible—the genus would be strictly monophyletic—but probably impractical. This paper presents a cladistic analysis of the tribe that differs from previous analyses in that it uses only strictly monophyletic (monogenomic) groups as terminal taxa; hybrids (heterogenomic groups) are shown as reticulations. Monophyletic groups can then be delimited to minimize the number of polyphyletic genera. A classification incorporating genomic information is derived from the phylogeny.     

THE GENOME ORIGIN OF TETRAPLOID SPECIES OF LEYMUS (POACEAE: TRITICEAE) INFERRED FROM VARIATION IN REPEATED NUCLEOTIDE SEQUENCES

To investigate the origin of the tetraploid species of Leymus Hochst., we examined variation in 26 repeated nucleotide sequence families isolated from four species of Triticeae. The genome relationships were determined by calculating repeated nucleotide sequence identity (RSI) between species. RSI is the ratio of the number of diagnostic bands (DBs) and diagnostic hybridization intensities (DIs) in Southern blots of a diploid taxon encountered in a polyploid species divided by the total number of the DBs and DIs of the diploid taxon (DB is a band in Southern blot observed in a single diploid taxon, and DI is the intensity of hybridization higher by at least one order of magnitude in a diploid taxon than in any other diploid taxon). The RSIs of Psathyrostachys Nevski with Leymus ranged from 0.92 to 0.95, which confirmed that the N genome of Psathyrostachys was involved in the phylogeny of Leymus. Since RSIs of other genera of Triticeae with Leymus varied from 0.00 to 0.17, it is unlikely that any of them contributed the second pair of Leymus genomes. RSIs were also calculated between Leymus and the lineage of Lophopyrum Löve-Thinopyrum Löve or the lineage of Lophopyrum-Thinopyrum-Pseudoroegneria (Nevski) Löve-Agropyron Gaertn. The RSIs were close to zero, which made it unlikely that the second pair of Leymus genomes originated from even an extinct species in these major lineages of Triticeae. Several lines of evidence were obtained that indicated that the second pair of Leymus genomes is also from Psalhyrostachys. The genomes of tetraploid species of Leymus were designated N₁N₁N₂N₂, rather than JJNN as proposed by other workers.     

Phylogenetic analysis of North American Elymus and the monogenomic Triticeae (Poaceae) using three chloroplast DNA data sets.

Although the monogenomic genera of the Triticeae have been analyzed in numerous biosystematic studies, the allopolyploid genera have not been as extensively studied within a phylogenetic framework. We focus on North American species of Elymus, which, under the current genomic system of classification, are almost all allotetraploid, combining the St genome of Pseudoroegneria with the H genome of Hordeum. We analyze new and previously published chloroplast DNA data from Elymus and from most of the monogenomic genera of the Triticeae in an attempt to identify the maternal genome donor of Elymus. We also present a cpDNA phylogeny for the monogenomic genera that includes more data than, and thus builds on, those previously published. The chloroplast DNA data indicate that Pseudoroegneria is the maternal genome donor to all but one of the Elymus individuals. There is little divergence among the Elymus and Pseudoroegneria chloroplast genomes, and as a group, they show little divergence from the rest of the Triticeae. Within the monogenomic Triticeae, the problematic group Thinopyrum is resolved as monophyletic on the chloroplast DNA tree. At the intergeneric level, the data reveal several deeper-level relationships that were not resolved by previous cpDNA trees.     

AN EVALUATION OF BAUM ET AL.'S ASSESSMENT OF THE GENOMIC SYSTEM OF CLASSIFICATION IN THE TRITICEAE

We have critically evaluated Baum, Estes, and Gupta's (1987) assessment of the genomic system of classification in the tribe Triticeae. They have raised some valid concerns about basing a taxonomic classification on genome relationships. However, some of their objections are ill-founded. Baum et al.'s contention that genome analysis can only supplement other criteria in assessing phylogeny is inaccurate. Genome analysis by itself has yielded extremely useful information on phylogenetic relationships in the Triticeae, and their assertion that an individual morphological trait be given the same weight as genomic relatedness is not tenable. Moreover, these authors have adopted cladistic algorithms in the Triticeae, an analysis appropriate only in groups where reticulation has not occurred. Evolution in the Triticeae is highly reticulate, the main sources of reticulation being allopolyploidy and homoploid recombinational speciation.     

Rusts (Uredinales) of Triticeae: evolution and extent of coevolution, a cladistic analysis

BAUM, B. R. & SAVILE, D. B. O., 1985. Rusts (Uredinales) of Triticeae: evolution and extent of coevolution, a cladistic analysis. Established evolutionary trends in Uredinales as a whole are reviewed, and primitive and advanced characters are presented. The rusts of all Poaceae arc presented in a table that strongly indicates Bambusoideae to be the oldest and Pooideae the youngest subfamily. The rusts of Triticeae and their ecogeography are outlined; the rusts of Cyperaceae, selected as an out-group, are beiefly summarized; and the available characters and character states for rusts of Triticeae are given. Host alternation complicates the analysis. The aerial host (never a grass) is ecologically associated with the unrelated telial (grass) host. There are no appropriate methods to permit analysis of the combined components: aecial host evolution, telial host evolution, rust evolution, and their coevolution. Also, several aecial hosts are unknown. Consequently it was necessary to omit aecial hosts from the analysis. Cladistic analysis of the rusts of Triticeae was performed using five methods and consisted of cycles of tree analysis and modification of character state trees. A cladogram put together from a Dollo and a Wagner cladogram was used as a basis for the classification of rusts given. Subsequently a cladistic analysis of genera of Triticeae, using presence/absence of rusts as characters (Brooks' approach) was performed. The Triticeae cladogram of Baum (1983) was also analysed. Distances between the cladogram generated by various methods and that of Baum were computed for each possible pair, using the method of Robinson & Foulds, and then the resulting distance matrix was reduced in dimensionality by principal components and non-metric multidimensional scaling. The results are discussed in light of the limitation of the analyses and the data. It is concluded that coevolution is limited and that frequent jumps to ecologically associated hosts explain the parallelism in evolution of rusts on Triticeae.     

Molecular phylogeny,analysis of character evolution,and submersible collections enable a new classification of a diverse group of gobies (Teleostei: Gobiidae: Nes subgroup), including nine new species and four new genera

The Nes subgroup of the Gobiosomatini (Teleostei: Gobiiformes: Gobiidae) is an ecologically diverse clade of fishes endemic to the tropical western Atlantic and eastern Pacific oceans. It has been suggested that morphological characters in gobies tend to evolve via reduction and loss associated with miniaturization, and this, coupled with the parallel evolution of adaptations to similar microhabitats, may lead to homoplasy and ultimately obscure our ability to discern phylogenetic relationships using morphological characters alone. This may be particularly true for the Nes subgroup of gobies, where several genera that are diagnosed by ‘reductive characters’ have been shown to be polyphyletic. Here we present the most comprehensive phylogeny to date of the Nes subgroup using mitochondrial and nuclear sequence data. We then evaluate the congruence between the distribution of morphological characters and our molecular tree using maximum‐likelihood ancestral state reconstruction, and test for phylogenetic signal in characters using Pagel's λ tree transformations (Nature, 401 , 1999 and 877). Our results indicate that all of the characters previously used to diagnose genera of the Nes subgroup display some degree of homoplasy with respect to our molecular tree; however, many characters display considerable phylogenetic signal and thus may be useful in diagnosing genera when used in combination with other characters. We present a new classification for the group in which all genera are monophyletic and in most cases diagnosed by combinations of morphological characters. The new classification includes four new genera and nine new species described here, many of which were collected from rarely sampled deep Caribbean reefs using manned submersibles. The group now contains 38 species in the genera Carrigobius gen. nov., Chriolepis, Eleotrica, Gobulus, Gymneleotris, Nes, Paedovaricus gen. nov., Pinnichthys gen. nov., Psilotris, and Varicus. Lastly, we provide a key to all named species of the Nes subgroup along with photographs and illustrations to aid in identification.     

我国淡水鱼类粘孢子虫的支序分类学研究

本研究选取15个主要特征对我国淡水鱼类23属粘孢子虫的支序分类进行了分析.结果表明,根据这15个特征构建的经典分支系统树与现有分类系统较为一致;而许多被分子系统学证明有争议的特征,如尾孢虫的尾突,孢子和极囊的形状等在研究粘孢子虫的系谱发育中仍然有着重要作用,剔除了上述特征的分支系统树与经典的分支系统树相比,存在许多缺陷.嗜碘泡是区分粘体虫和碘泡虫的主要特征,然而剔除嗜碘泡特征的分支系统树与经典的分支系统树区别不大,因此,我们建议在这一方面和国际学术界统一起来,即不再把嗜碘泡作为区分碘泡虫和粘体虫的主要特征.     

Morphological variation and genome constitution in some perennial Triticeae

JARVIE, J. K. & BARKWORTH, M. E., 1992. Morphological variation and genome constitution in some perennial Triticeae. A numerical analysis of species of five genomically defined genera of the Triticeae was undertaken, based on 42 morphological characters and 142 operational taxonomic units (OTUs). The primary goal was to determine the degree of congruence between morphological variation and genomic constitution. The second goal was to determine which existing supraspecific classification, if any, best reflected the morphological variation encountered. The five genera investigated were Thinopyrum (J genome), Lophopyrum (E genome), Pseudoroegneria (S genome), Trichopyrum (EES genome) and Elytrigia (SJE/SSX genome). Both principal co-ordinate and cluster analysis of the data placed the OTUs in supraspecific groups that reflected their genomic constitution. Monogenomic taxa were clearly separated. Allotetraploids between the E and S genomes were situated between E and S monogenomic taxa. Allotetraploids between the J and E genomes were situated closest to J genome taxa. The EES taxa of Trichopyrum were placed closest to Lophopyrum. OTUs of Elytrigia overlapped those of Pseudoroegneria , but not those of Lophopyrum or Thinopyrum.     

Dynamics of Tandem Repetitive Afa-Family Sequences in Triticeae, Wheat-Related Species

The Afa-family sequences in wheat-related species, Triticeae, are tandem repetitive sequences of 340 bp. All the analyzed Triticeae species carried the sequences in their genomes, though the copy numbers varied about 100-fold among the species. The nucleotide fragments amplified by PCR were cloned and sequenced, and their behavior in the evolution of Triticeae was analyzed by the neighbor-joining (NJ) method. The sequences in genomes with many copies of this family clustered at independent branches of the phylogenic tree, whereas the sequences in genomes with a few copies did not. This may suggest that Afa-family sequences had amplified several times in the evolution of Triticeae, each using a limited number of different master copies. In addition, the sequences of the A and B genomes of hexaploid common wheat indicated that the Afa-family sequences had not evolved in a concerted manner between the genomes. Furthermore, the sequences of each chromosome of the D genome of this species indicated that the sequences had amplified on all over the D-genome chromosomes in a short period. Received: 1 September 1997 / Accepted: 19 January 1998     

Comparison of Acetyl-CoA carboxylase 1 (Acc-1) gene diversity among different Triticeae genomes

It has widely been documented that life form and mating system have significant influences on genetic diversity. In the tribe Triticeae, several genera contain both annual and perennial species, whereas other genera comprise strictly annual or perennial species. It was suggested that Triticeae annuals have originated from Triticeae perennials. The present study aims to analyze nucleotide diversity of Acc-1 gene among different Triticeae genomes, and attempts to link effects of life history (annuals and perennials) and mating systems. The nucleotide diversity of 364 Acc-1 sequences in Triticeae species was characterized. The highest estimates of nucleotide diversity values (π = 0.01919, θ = 0.03515) were found for the Ns genome among the genomes analyzed. Nucleotide diversities in the D genome and Ns genome of polyploids are higher than those in respective genomes of diploids, while in the St genome of polyploids, it is lower than that in the St genome of diploids. The averaged π value (0.013705) in the genomes of perennials is more than twice of the value (0.00508) in the genomes of annuals. The averaged π value (0.01323) in the genomes of outcrossing species is two-fold of the value (0.005664) in the genomes of selfer. Our results suggested that the evolutionary history and mating system may play an important role in determining nucleotide diversity of Acc-1 gene in each genome.     

禾本科牧草的同工酶分析

本文分析了23种禾本科牧草的酯酶同工酶和过氧化物酶同工酶。结果表明,如果统一取材标准及实验条件严格,酶谱资料是稳定可比较的,有一定的系统分类价值。酶谱并结合其它资料证明了成立鼠茅属(Vulpia)的合理性。酶谱资料还表明,黑麦草属(Lolium)可能是小麦族和羊茅族相互联系的桥梁。根据酶谱距离的资料,讨论了小麦族的某些属间关系。例如,作者发现,酶谱资料显示出鹅观草属与披碱草属赖草与披碱草属之间有更近的亲缘关系。     

山东小麦族植物叶表皮微形态的研究

利用光学显微镜,对山东小麦族5属9种植物的叶片下表皮微形态特征进行了研究。叶片下表皮微形态在属间差异明显,可作为分属的参考依据;山东5种鹅观草属植物的叶片下表皮微形态可分为两种类型,这与形态上划分的拟披碱草组和犬草组相一致。     

NEW CLADID AND FLEXIBLE CRINOIDS FROM THE MISSISSIPPIAN (TOURNAISIAN, IVORIAN) OF ENGLAND AND WALES

Abstract:  The modern study of fossil crinoids began with J. S. Miller who, in 1821, described specimens from southern England, nearby Wales and other regions, and named several common Early Carboniferous genera. Later, in 1950–60, James Wright monographed all known Early Carboniferous crinoids from the British Isles. In spite of such previous scrutiny, we recognize here two new genera among species already described: Glamorganocrinus gen. nov. (type species: Ophiurocrinus gowerensis Wright, 1960) from South Wales and Mendipocrinus gen. nov. (type species: Poteriocrinus latifrons Austin and Austin, 1847) from southern England. These new genera increase the number of advanced cladid genera in the Ivorian Substage of the Tournaisian in western Europe to 18, and the total number of crinoid genera to 36. A review of species assigned to Mespilocrinus has led to the recognition of M. granulifer De Koninck and LeHon, 1854 as a nomen dubium. A new species of Mespilocrinus , M. wrighti sp. nov., is described from the Ivorian of South Wales; this is the most highly derived species of the genus, as based on a phylogenetic analysis including ten species and 13 characters, with Pycnosaccus as the outgroup. A single, well-ordered tree resulted from this analysis. Interpretation of this tree suggests that the centre of evolution for Mespilocrinus was North America, where three species appeared during the Kinderhookian (early Tournaisian), rapidly achieving morphological disparity within the genus. This radiation event was part of the overall explosive radiation of crinoids following the Late Devonian mass extinction event when crinoid diversity was at a global minimum during the Frasnian. Recovery began during the Famennian, followed by an explosive radiation in the Tournaisian.     

鹅观草属、披碱草属、猬草属和仲彬草属物种的RAMP分析及系统学意义

对鹅观草属、披碱草属、猬草属和仲彬草属4属23个物种进行了RAMP分析。结果表明属间变异极大,多态性极高。31个引物组合产生的286条DNA扩增片段均具有多态性。聚类分析显示鹅观草属、披碱草属、猬草属和仲彬草属物种各自聚为一类;Roegneria alashanica、R．elytrigioides和R．magnticaespes聚类在一起;猬草属的模式种Hystrix patula与披碱草属物种聚类在一起,而Hystrix duthiei和H．longearistata单独聚为一类;形态相似、染色体组相同、地理分布一致的物种聚类在一起。本研究结果基本上同形态学和细胞学研究结果相吻合,将鹅观草属、披碱草属和仲彬草属作为属分类等级处理比较恰当,而猬草属的系统地位有待进一步确认。RAMP标记可作为评价多年生小麦族物种遗传多样性和亲缘关系的一种分子标记技术。     

PHYLOGENY OF THE RUBIACEAE AND THE LOGANIACEAE: CONGRUENCE OR CONFLICT BETWEEN MORPHOLOGICAL AND MOLECULAR DATA?

Phylogenetic analyses of 33 genera of Rubiaceae were performed using morphological and a few chemical characters. Parsimony analysis based on 29 characters resulted in eight equally parsimonious trees, with a consistency index of 0.40 and a retention index of 0.69. These results were compared to a phylogenetic analysis of the same genera based on chloroplast DNA restriction site data. There are discrepancies between the two analyses, but if we consider groupings reflected in the present classification there is much congruency. With the exception of four genera, all the genera are positioned in the same group of taxa in the two analyses. Clades of taxa representing three of the four subfamilies (~the Antirheoideae, ~the Rubioideae, and the ~Ixoroideae) are monophyletic, while the fourth subfamily Cinchonoideae is shown to be paraphyletic. Both analyses support a widened tribe Chiococceae, including the former subtribe Portlandiinae (Condamineeae). Furthermore, in both analyses the tribe Hamelieae is placed outside the subfamily Rubioideae where it is now housed. In search for the most plausible sister group to the Rubiaceae, the genus Cinchona (Rubiaceae) was analyzed together with 13 genera of the Loganiaceae, Nerium (Apocynaceae), and Exacum (Gentianaceae). Cornus (Comaceae), Olea (Oleaceae), and these two genera together were used as outgroups. The analysis, including 25 characters, 16 taxa, and with Cornus and Olea together as an outgroup, resulted in four equally parsimonious trees, with a consistency index of 0.53 and a retention index of 0.62. The non-Loganiaceae taxa Cinchona (Rubiaceae), Nerium (Apocynaceae), and Exacum (Gentianaceae) were all found to have their closest relatives within the Loganiaceae indicating that the Loganiaceae are paraphyletic and ought to be reclassified. As a result of the morphological data the most plausible sister group to the Rubiaceae is the tribe Gelsemieae of the Loganiaceae.