A search for the phylogenetic position of the seven-son flower (Heptacodium, Dipsacales): Combining molecular and morphological evidence

A first report on the problematic phylogenetic position ofHeptacodium (2 spp.; China) using molecular data from chloroplast DNA is presented. Amplification of ORF2280 homolog region was executed in a number of representative taxa in order to determine ifHeptacodium shows similar structural rearrangements as other Dipsacales. DNA sequences ofndhF were generated to clarify the phylogenetic position ofHeptacodium among Caprifoliaceae (s.l.). Six outgroup taxa and fifteen representatives of Dipsacales were sampled and more than 2100 basepairs ofndhF sequence were used in a cladistic analysis. Parsimony analysis produced two shortest trees and showedHeptacodium as sister to all members of Caprifoliaceae (s.str.), although weakly supported. Additionally, trees were constructed withndhF data supplemented with availablerbcL sequences and a morphological data set. Results of all analyses support an unresolved basal position forHeptacodium among Caprifoliaceae (s.l.), which in part explains the difficulty experienced previously in classifying the genus.     

Phylogeny and Phytogeography of the Betulaceae (to be continued)

In the present thesis, a detailed review of the literature was given on the Betulaceae. Some new data was provided based on the author’s studies in order to analyze various characters, such as inflorescence, flower, pollen and leaf epidermis, among the genera treated. The polarity of the characters was determined according to the criteria of outgroup comparison and compatibility analysis. A cladistic analysis was made using the methods of Maximal Same Steps and Minimal Parallel Evolution developed by Xu (1993). The generic distributions in both modern and fossil times were outlined, and their distribution center, place and time of origin and the way of dispersal were discussed. An attempt was made to discuss early differentiation, geographical radiation and morphological evolution of the family on the background of paleogeography and paleoclimatology, tracing back as far as the Late Cretaceous and Early Tertiary. Finally, supraspecific taxa, from section to tribe, were systematically arranged.     

旌节花科及其相关类群的分支分析

选取生长习性、植物形态、木材解剖、花的形态结构、花粉特征以及胚胎学和染色体数目等共72个性状,采用最大简约法（Maximum Parsimony,MP)对旌节花科及其相关类群五桠果科、猕猴桃科、山茶科、金莲木科和省沽油科等进行分支分析。并用靴带检验法（Bootstrap)计算内部分支的支持率。分支图表明,旌节花科与省沽油科组成姊妹群,靴带支持率为79％,表明旌节花科与省沽油科具有最为密切的关系。旌节花科与猕猴桃科的关系次之,旌节花科和省沽油科与猕猴桃科关系的靴带支持率为58％。然后是山茶科。而旌节花科与金莲木科和五桠果科的关系则依次疏远。这与我们在孢粉学和胚胎学研究中所得的结论在某些方面是基本一致的。与Nandi等人用形态学数据和分子数据分析得到的结论也比较吻合,他们的结论也认为旌节花科与省沽油科具有比较密切的关系。只是他们把五桠果科和金莲木科摆在更近的位置,而山茶科和猕猴桃科则放在较疏远的位置上。     

中国慈姑属系统发育的研究

本文研究了中国慈姑属植物间的系统发育关系。选取了12个与该属系统发育有较重要关系的特征,将8个已知分类群与外类群刺果泽泻属进行了比较。应用数量分支分析的Farris-Wagner方法,建立了中国慈姑属系统发育分支图。讨论了各分类群间的系统发育关系、该属起源和数量分支分析方法等问题。     

Phylogenetic Analysis of the Family Taxodiaceae

In the present paper,both cladistic analysis and phenetic analysis were conducted to evaluate the phylogenetic relationships of the Taxodiaceae based on an extensive literature review and study of herbarium． In the cladistic analysis,the Sciadopityaceae was chosen as outgroup．The polarity of characters was determined mainly according to outgroup comparison,fossil evidence and generally accepted viewpoints of morphological evolution．By the result of compatibility analysis,character 2(leaf type),which possessed a much higher coefficient than others whether or not its polarity was altered,was deleted． Finally,a data matrix consisting of all the extant nine genera and 24 characters was analyzed using Maximal Same Step Method,Synthetic Method,Evolutionary Extremal Aggregation Method and Minimal Parallel Evolutionary Method,and four cladograms were generated,of which only the most parsimonious one (Fig．1)was presented for discussion. The cladogram shows that the Taxodiaceae are assorted along five lines of evolution： 1)Metasequoia;2)Sequoiadendron,Sequoia;3)Cryptomeria;4)Glyptostrobus and Taxodium;5)Cunninghamia,Athrotaxis and Taiwania． Ten genera(including Sciadopitys)and 59 characters were used in the phenetic analysis．The phenogram(Fig．2)indicates that Sciadopitys is a very distinct group with remote affinity to the other genera,and the Taxodiaceae are divided into four groups：1)Sequoia,Sequoiadendron;2)Athrotaxis,Cunninghamia and Taiwania;3)Cryptomeria,Glyptostrobus and Taxodium;4)Metasequoia． Based primarily on the result of cladistics,with reference to that of phenetics,the main conclusions were drawn as follows：(1)Generic relationships：Cryptomeria should be considered the most primitive genus in the extant groups of the Taxodiaceae. Glyptostrobus and Taxodium, close to Cryptomeria, are sister taxa and relatively primitive groups. Sequoiadendron and Sequoia are closely related and intermediate advanced. Metasequoia is a more or less isolated taxon, relatively close to Sequoiadendron and Sequoia. Cunninghamia. Athrotaxis and Taiwania might represent a single lineage and form a very advanced group, of which Taiwania may be the most specialized. (2) Systematic treatments: The authors support the viewpoint that Sciadopitys should be treated as an independent family, and suggest that the Taxodiaeae should be divided into five tribes. Systematic arrangements are as follows: Taxodiaceae Warming Trib. 1. Cryptomerieae Vierhapper Gen. 5. Sequoia Endl. Gen. 1. Cryptomeria D. Don Trib. 4. Metasequoieae Pilger et Melchior Trib. 2. Taxodieae Benth. et Hook. Gen. 6. Metasequoia Miki ex Hu et Cheng Gen. 2. Glyptostrobus Endl. Trib. 5. Cunninghamieae Zucc. Gen. 3. Taxodium Rich. Gen. 7. Cunninghamia R. Br. Trib. 3. Sequoieae Wettstein Gen. 8. Athrotaxis D. Don Gen. 4. Sequoiadendron Buchholz Gen. 9. Taiwania Hayata     

Comparison of the Cladograms Produced by Li's Method and Farris' Method

In order to avoid producing many equally most parsimonious trees, Li (1990) developed a new cladistic method, the Median Elimination Series (MES), to construct a single cladogram for a given data set. However, we found that Li's method can produce more than one tree if two or more taxa have the same advancement index (which is the total number of apomorphies for a taxon in a given data set), because there is no objective method to decide which taxon should be connected first and different orders of connection can produce different trees. Li claimed that the result produced by his method did not apply the principle of simplicity (parsimony). Nevertheless, Zhang (1991) recognised that Li's method actually accepted the principle of parsimony. Here we demonstrated that Li's method also can produce the minimum-length trees. We conclude that Li's method could produce more than one tree and the tree(s) may be the minimum-length possible. However, the length of tree(s) depends on the order of connection of the taxa. The major problems in using Li's methodare discussed.     

A New Method for Cladistic Analysis—Median Elimination Series (MES)

The use of parsimony (or the principle of simplicity) in phylogenetic inference is reviewed. The major problem in using parsimony for phylogenetic reconstruction is that neither a single solution for a given set of data nor the most parsimonious tree could be provided. Therefore, based on recognition and judgement of similarity of organisms by Hennig's advanced character (1965) and some particular principles from evolutionary theory of Darwinism accepted by many systematists as general truths (Bonde 1977; Wiley 1975; Gaffrey 1979), the author has developed a new method, Elimination Series through Median Selection (Median Elimination Series, MES for short), for phylogenetic analysis. In addition to using the advanced characters for understanding the relationships between taxa, MES emphasizes that the mosaic characters including both primitive and advanced in an array of characters play an important part in determining the nodes or branches and distinguishing the taxa.The author considers median units as ancestors in a phylogenetic tree like Farris, but the concept and algorithm of “median” differ from Farris' (1970) in: (1) The author's median involves the top taxon and unplaced one, but Farris' median does the top taxon, its ancestor as well as unplaced one; (2) The median taken by the author is of common value or the least one among the associated characters of two taxa. However, the median taken by Farris is median numerical value among the three (3) The median or median unit called by the author is the numerical value of the relatively primitive character or taxon between the advanced characters or the taxa stood apart from the original position. Farris' one is the median position or number in the center of three taxa or its associated characters. The author recognizes that reversion of characters is possible and obtains the knowledge of it from observation and analysis of characters of organisms or scientific experiment and distinguished through analysis of morphocline and co-variation in a series of taxa, but not from induction only by mathematical model based on the principle of simplicity. The author divides co-variation into 4 types: 1. Progressive co-variation. Transformation series of characters A and a is as follows: A → A' a → a' reversed co-variation. Transformation series of characters A and a is as follows: A ← A' a ← a' 3. Progression-reversion co-variation. Transformation series of characters A and a is follows: A → A' a ← a' 4. Reversion-progression co-variation. Transformation series of characters A and a is as follows: A ← A' a → a' The characters next to the arrows should be advanced. Co-variation for most of the species of Cissus from China belongs to the type 1 and that for C. repanda Vahl. to the type 3, without types 2 and 4. In determining the progressive co-variation, reverse evolution of character could be distinguished through the analysis of morphocline and co-variation. The author has recognized two types of cyclic polarity, including unidirectional and bidirectional ones. For the former, the character may return back to the original state through more than one step. In fact, this is a complex reversion. For the latter, the character may reach a advanced state from the original one via two different ways. In fact, this is special progressive transformation series and it may often occur in complex reticulate evolution as a small net, for example, in evolution of leaf fragment and others of angiosperms (Meyen 1973). The cyclic polarity in C. repanda Vahl. is bidirectional (see transformation series 11 of the characters in Cissus). Transformation series of All the characters have been determined on the basis of analysis of morphocline, co-variation and cyclic polarity. In this paper, the three steps of understanding phylogenetic system are developed: (1) recognition of homologous characters; (2) discovery of internal relationships between homologous characters in order to obtain transformation series or phylogeny of homologous characters; (3) discovery of internal relationships between phylogenies of homologous characters in order to get a phylogenetic system of organisms or approaching understanding essence of evolution. The result inferred by MES is based on some principles of evolution from Darwin and Hennig but not judged by the principle of simplicity or parsimony from Popper (1960, 1968). The statement in this paper attempts to show that if a dilemma in modern cladistics could be solved, its principles must be reconsidered. Decontaminated thianthrene disproportion. 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Molecular phylogeny of the assassin bugs (Hemiptera: Reduviidae), based on mitochondrial and nuclear ribosomal genes

The first comprehensive cladistic analysis of Reduviidae, the assassin bugs, based on molecular data is presented and discussed in the context of a recently-published morphological analysis. Assassin bugs are essential components of ecosystems, but also important in agriculture and medicine. Sampling included 94 taxa (89 Reduviidae, 5 outgroups) in 15 subfamilies and 24 tribes of Reduviidae and is based on 3300 base pairs of mitochondrial (16S) and nuclear (18S, 28SD2, 28SD3-5) ribosomal DNA. Partitions of the dataset were aligned using different algorithms implemented in MAFFT and the combined dataset was analyzed using parsimony, partitioned maximum likelihood and partitioned Bayesian criteria. Clades recovered in all analyses, independent of alignment and analytical method, comprise: Cimicomorpha and Reduviidae; Hammacerinae; Harpactorinae; Apiomerini; Peiratinae; Phymatinae; Salyavatinae; Triatominae; Phymatinae + Holoptilinae; the higher Reduviidae (Reduviidae excluding Hammacerinae and the Phymatine Complex); Ectrichodiinae + Tribelocephalinae; (Triatominae + Zelurus) + Stenopodainae. Hammacerinae are rejected as sister group to all remaining Reduviidae in all analyses, as is the monophyly of Reduviinae, Emesinae and Harpactorini. High support values for Triatominae imply that blood-feeding has evolved only once within Reduviidae. Stenopodainae and part of Reduviinae are discussed as close relatives to Triatominae.     

Species-level diversification of African dwarf crocodiles (Genus Osteolaemus): A geographic and phylogenetic perspective

The taxonomy of the African dwarf crocodile (genus Osteolaemus) has been disputed since a novel morphotype was discovered in the early 20th Century. Because this poorly-known reptile is widely hunted throughout the forests of Central and West Africa, resolving the existence and extent of taxonomic units has important management and conservation implications. Lack of molecular data from individuals of known origin and historical disagreement on diagnostic morphological characters have hindered attempts to settle one of the most important taxonomic questions in the Crocodylia. In an effort to clarify the evolutionary relationships among dwarf crocodiles, we sequenced three mitochondrial and two nuclear genes using a large sample of dwarf crocodiles from known localities across major drainage basins of forested Africa. Concordant results from Bayesian, maximum likelihood, maximum parsimony and population aggregation analytical methods support a previously recognized division of the dwarf crocodile into a Congo Basin form (O. osborni) and a West African form (Osteolaemus tetraspis), but also reveal a third diagnosable lineage from West Africa warranting recognition as an separate taxonomic unit. Corrected genetic distances between geographic regions ranged from 0.2% to 0.6% in nuclear fragments and 10.0 to 16.2% in mitochondrial COI. Population aggregation, using fixed and alternate character (nucleotide) states to cluster or divide populations, recovered 232 such molecular characters in 4286 bp of sequence data and unambiguously aggregated populations into their respective geographic clade. Several previously recognized morphological differences coincide with our molecular analysis to distinguish Congo Basin crocodiles from the Ogooué Basin and West Africa. Discrete morphological characters have not yet been documented between the latter two regions, suggesting further work is needed or molecular data may be required to recognize taxonomic divisions in cases where putative species are morphologically cryptic. This study highlights the importance of using widespread taxon sampling and a multiple evidence approach to diagnose species boundaries and reveal cryptic diversity.