中国榕属榕亚属植物的系统发育初探

对分布于中国的榕亚属植物的15个种和2个变种(分别代表榕亚属的3个组)的nrDNA的ITS序列和系统发育关系进行分析。结果表明,榕亚属是非单系起源,其中榕组构成了一个独立的单系群,与无花果亚属有较近的亲缘关系,而与榕亚属其它组间并未表现出近缘关系。榕亚属的其它5个组构成一单系群并得到中度的支持率。来自中国的种类分别聚在相应的组内。但环纹榕组被分成2个单支,其中来自中国的大叶水榕(F.glaberrima)和环纹榕(F.annulata)构成一个分支,二者表现较近的亲缘关系。榕亚属的亚洲特有组印度榕组在ITS树中聚在环纹榕组的另一个分支中,但它与此组其它种的亲缘关系并不清楚。     

Biogeographical and phylogenetic origins of African fig species (Ficus section Galoglychia)

Ficus section Galoglychia (subgenus Urostigma; Moraceae) includes 72 species restricted to the African floristic region (a few extending to the Arabian Peninsula and Socotra). We present the first molecular phylogenetic analysis of the section including 56 ingroup (representing 44 species) and three outgroup taxa, to investigate its monophyly, classification and evolution. We used sequence data from the nuclear ribosomal internal and external transcribed spacers (ITS and ETS). Our results suggest that section Galoglychia is paraphyletic to the neotropical section Americana, although this is not supported by bootstrap analysis and only weakly supported by Bayesian posterior probabilities. Maximum parsimony analysis conflict with maximum likelihood and Bayesian analyses with respect to the closest relatives of section Americana in Africa. The subsections of section Galoglychia proposed by Berg [Berg, C.C., 1986. Subdivision of Ficus subg. Urostigma sect. Galoglychia (Moraceae). Proc. Kon. Ned. Akad. Wetensch., Ser. C, 89, 121-127] are generally supported. We find two major clades of section Galoglychia within Africa possibly corresponding to two main centres of diversity. One clade comprises members of subsections Platyphyllae and Chlamydodorae, which are more concentrated in Eastern Africa, and extend to Madagascar and neighbouring archipelagos (Comores, Mascarenes, Aldabra Islands and Seychelles). The other main clade includes members of subsections Caulocarpae, Cyathistipulae, Crassicostae and Galoglychia, which are concentrated in West and Central Africa.     

Anonymous and EST-based microsatellite DNA markers that transfer broadly across the fig tree genus (Ficus, Moraceae)

? Premise of the study: We developed a set of microsatellite markers for broad utility across the species-rich pantropical tree genus Ficus (fig trees). The markers were developed to study population structure, hybridization, and gene flow in neotropical species. ? Methods and Results: We developed seven novel primer sets from expressed sequence tag (EST) libraries of F. citrifolia and F. popenoei (subgen. Urostigma sect. Americana) and optimized five previously developed anonymous loci for cross-species amplification. The markers were successfully tested on four species from the basal subgenus Pharmacosycea sect. Pharmacosycea (F. insipida, F. maxima, F. tonduzii, and F. yoponensis) and seven species of the derived subgenus Urostigma (F. citrifolia, F. colubrinae, F. costaricana, F. nymphaeifolia, F. obtusifolia, F. pertusa, and F. popenoei). The 12 markers amplified consistently and displayed polymorphism in all the species. ? Conclusions: This set of microsatellite markers is transferable across the phylogenetic breadth of Ficus, and should therefore be useful for studies of population structure and gene flow in approximately 750 fig species worldwide.     

Molecular phylogenetic study of the heterotrophic dinoflagellate genus Protoperidinium (Dinophyceae) inferred from small subunit rRNA gene sequences

In the present study, we investigated the intrageneric and intergeneric phylogenetic relationships of the heterotrophic marine dinoflagellate genus Protoperidinium. Using single‐cell polymerase chain reaction methods, we determined small subunit ribosomal RNA gene sequences for 10 Protoperidinium species belonging to four sections and two subgenera. Phylogenetic trees were constructed using maximum parsimony, neighbor joining and maximum likelihood methods. We found intraspecific variability of small subunit rDNA sequences in Protoperidinium conicum (Gran) Balech, Protoperidinium crassipes (Kofoid) Balech and Protoperidinium denticulatum (Gran et Braarud) Balech, but not in other species. The small subunit rDNA phylogeny revealed that the genus is monophyletic, but its phylogenetic position within the Dinophyceae could not be determined because of ambiguous basal topologies. Within the genus Protoperidinium, species of the subgenus Archaeperidinium with two anterior intercalary plates (2a) were shown to be monophyletic, but species of the subgenus Protoperidinium with three anterior intercalary plates (3a) were resolved as paraphyletic. The sections Avellana, Divergentia and Protoperidinium were shown to be monophyletic, while the section Conica was paraphyletic. Based on the trees obtained in the present study, most of the traditionally defined sections are supported by molecular phylogeny. It was also indicated that the section Avellana evolved from one of the Conica‐type dinoflagellates.     

Molecular phylogenies of figs and fig-pollinating wasps in the Ryukyu and Bonin (Ogasawara) islands, Japan

The interaction between figs (Ficus, Moraceae) and fig-pollinating wasps (Chalcidoidea, Agaonidae) is one of the most specific mutualisms, and thus is a model system for studying coevolution and cospeciation. In this study we focused on figs and their associated fig-wasps found in the Ryukyu and Bonin (Ogasawara) Islands, Japan, because it has been suggested that breakdown in the specificity may occur in islands or at edge of a species' distribution. We collected 136 samples of 15 native fig species and 95 samples of 13 associated fig-wasps from all major islands in the Ryukyu Islands, including two fig species and one fig-wasp species endemic to the Bonin Islands. We performed molecular phylogenetic analyses using plastid DNA and nuclear ITS sequences for the figs and nuclear 28S rRNA and mitochondrial COI genes for the fig-wasps to investigate the interspecific phylogenies and intraspecific variation within the mutualism. Our phylogenetic analyses using multiple samples per species show the single clade of each fig (except the Bonin endemic species) and fig-pollinating wasp species. Fig species belonging to the same subgenera formed well-supported clades in both plastid and ITS trees, except for the subgenus Urostigma. Likewise, fig wasps emerging from host fig species belonging to the same subgenera formed mostly well supported clades in both 28S and COI trees. Host specificity between the figs and fig-wasps functions strictly in these islands. There was very little sequence variation within species, and that no major geographic structure was found. The two Bonin endemic species (F. boninsimae and F. nishimurae) or their common ancestor and the associated fig-wasps (Blastophaga sp.) are apparently derived from F. erecta and its associated fig-wasps (B. nipponica), respectively, and probably migrated from the Ryukyu Islands.     

Phylogenetic relationships and infrageneric classification of Epidendrum subgenus Amphiglottium (Laeliinae, Orchidaceae)

Epidendrum L. is the largest genus of Orchidaceae in the Neotropical region; it has an impressive morphological diversification, which imposes difficulties in delimitation of both infrageneric and interspecific boundaries. In this study, we review infrageneric boundaries within the subgenus Amphiglottium and try to contribute to the understanding of morphological diversification and taxa delimitation within this group. We tested the monophyly of the subgenus Amphiglottium sect. Amphiglottium, expanding previous phylogenetic investigations and reevaluated previous infrageneric classifications proposed. Sequence data from the trnL-trnF region were analyzed with both parsimony and maximum likelihood criteria. AFLP markers were also obtained and analyzed with phylogenetic and principal coordinate analyses. Additionally, we obtained chromosome numbers for representative species within the group. The results strengthen the monophyly of the subgenus Amphiglottium but do not support the current classification system proposed by previous authors. Only section Tuberculata comprises a well-supported monophyletic group, with sections Carinata and Integra not supported. Instead of morphology, biogeographical and ecological patterns are reflected in the phylogenetic signal in this group. This study also confirms the large variability of chromosome numbers for the subgenus Amphiglottium (numbers ranging from 2n = 24 to 2n = 240), suggesting that polyploidy and hybridization are probably important mechanisms of speciation within the group.     

Molecular phylogenetics of the genus Ceratitis (Diptera: Tephritidae)

The Afrotropical fruit fly genus Ceratitis MacLeay is an economically important group that comprises over 89 species, subdivided into six subgenera. Cladistic analyses of morphological and host use characters have produced several phylogenetic hypotheses for the genus. Only monophyly of the subgenera Pardalaspis and Ceratitis (sensu stricto) and polyphyly of the subgenus Ceratalaspis are common to all of these phylogenies. In this study, the hypotheses developed from morphological and host use characters are tested using gene trees produced from DNA sequence data of two mitochondrial genes (cytochrome oxidase I and NADH-dehydrogenase subunit 6) and a nuclear gene (period). Comparison of gene trees indicates the following relationships: the subgenus Pardalaspis is monophyletic, subsection A of the subgenus Pterandrus is monophyletic, the subgenus Pterandrus may be either paraphyletic or polyphyletic, the subgenus Ceratalaspis is polyphyletic, and the subgenus Ceratitis s. s. might not be monophyletic. In addition, the genera Ceratitis and Trirhithrum do not form reciprocally monophyletic clades in the gene trees. Although the data statistically reject monophyly for Trirhithrum under the Shimodaira-Hasegawa test, they do not reject monophyly of Ceratitis.     

Phylogenetic relationships of functionally dioecious FICUS (Moraceae) based on ribosomal DNA sequences and morphology

Figs (Ficus, Moraceae) are either monoecious or gynodioecious depending on the arrangement of unisexual florets within the specialized inflorescence or syconium. The gynodioecious species are functionally dioecious due to the impact of pollinating fig wasps (Hymenoptera: Agaonidae) on the maturation of fig seeds. The evolutionary relationships of functionally dioecious figs (Ficus subg. Ficus) were examined through phylogenetic analyses based on the internal transcribed spacer (ITS) region of nuclear ribosomal DNA and morphology. Forty-six species representing each monoecious subgenus and each section of functionally dioecious subg. Ficus were included in parsimony analyses based on 180 molecular characters and 61 morphological characters that were potentially informative. Separate and combined analyses of molecular and morphological data sets suggested that functionally dioecious figs are not monophyletic and that monoecious subg. Sycomorus is derived within a dioecious clade. The combined analysis indicated one or two origins of functional dioecy in the genus and at least two reversals to monoecy within a functionally dioecious lineage. The exclusion of breeding system and related characters from the analysis also indicated two shifts from monoecy to functional dioecy and two reversals. The associations of pollinating fig wasps were congruent with host fig phylogeny and further supported a revised classification of Ficus.     

Phylogenetic relationships of fig wasps pollinating functionally dioecious Ficus based on mitochondrial DNA sequences and morphology

The obligate mutualism between pollinating fig wasps in the family Agaonidae (Hymenoptera: Chalcidoidea) and Ficus species (Moraceae) is often regarded as an example of co-evolution but little is known about the history of the interaction, and understanding the origin of functionally dioecious fig pollination has been especially difficult. The phylogenetic relationships of fig wasps pollinating functionally dioecious Ficus were inferred from mitochondrial cytochrome oxidase gene sequences (mtDNA) and morphology. Separate and combined analyses indicated that the pollinators of functionally dioecious figs are not monophyletic. However, pollinator relationships were generally congruent with host phylogeny and support a revised classification of Ficus. Ancestral changes in pollinator ovipositor length also correlated with changes in fig breeding systems. In particular, the relative elongation of the ovipositor was associated with the repeated loss of functionally dioecious pollination. The concerted evolution of interacting morphologies may bias estimates of phylogeny based on female head characters, but homoplasy is not so strong in other morphological traits. The lesser phylogenetic utility of morphology than of mtDNA is not due to rampant convergence in morphology but rather to the greater number of potentially informative characters in DNA sequence data; patterns of nucleotide substitution also limit the utility of mtDNA findings. Nonetheless, inferring the ancestral associations of fig pollinators from the best-supported phylogeny provided strong evidence of host conservatism in this highly specialized mutualism.     

Molecular phylogeny and systematic in the genus Brachycaudus (Homoptera: Aphididae): insights from a combined analysis of nuclear and mitochondrial genes

Phylogenetic relationships among members of the Aphid genus Brachycaudus (Homoptera: Aphididae) were inferred from partial sequences of mitochondrial cytochrome B oxidase (CytB), two partial fragments of mitochondrial cytochrome C oxidase subunit I (COI) and the internal transcribed spacer II (ITS2) of ribosomal DNA. Twenty-nine species, with several specimens per species, were included, representing all the historically recognized species-groups and subgenera used in the genus except the monospecific subgenus Mordvilkomemor. Results indicate that the genus Brachycaudus is a well-supported monophyletic group. While our results validate the monophyly of subgenera Thuleaphis , Appelia and Brachycaudus s. str. , they reveal two discrepancies in the classical taxonomy. First, the monotypic subgenus Nevskyaphis does not appear valid. Second, the traditionally defined Acaudus subgenus is not monophyletic. On the other hand, our phylogenetic trees corroborate Andreev's recent definition of Acaudus and Brachycaudina. However, they clearly show that the subgenera Prunaphis , Nevskyaphis and Scrophulaphis as defined by this author do not form monophyletic groups. Our results also highlight a highly supported clade that has not been discussed by previous authors; this clade could form a new subgenus, the subgenus Nevskyaphis . Finally, our study shows that molecular data and morphology meet the same limits in delimiting species groups and species themselves. Species groups in which taxonomic treatment is difficult are polytomous. Furthermore, except for one node clustering Brachycaudus s. str . and Appelia, intersubgeneric relationships remain poorly resolved even when several genes are added to the phylogenetic analysis. These results, together with previous studies in other aphid groups suggest that diversification might have been a rapid process in aphids.     

Rapid speciation and the evolution of hummingbird pollination in neotropical Costus subgenus Costus (Costaceae): evidence from nrDNA ITS and ETS sequences

We estimate phylogenetic relationships and the biogeographic and pollination history of Costus subgenus Costus (Costaceae) using sequence data from the internal and external transcribed spacer (ITS and ETS) regions of 18S-26S nuclear ribosomal DNA. The African members of the subgenus form a series of lineages basal to a monophyletic neotropical species radiation. The neotropical species have large, showy flowers visited by either euglossine bees or hummingbirds. The hummingbird pollination syndrome is supported as a derived character state from the bee pollination syndrome, and we estimate that it has evolved independently seven or more times in the neotropics. A molecular clock approach suggests that diversification of the neotropical clade has been recent and rapid and that it coincides with dramatic climatic and geologic changes, Andean orogeny, and the closing of the Panama isthmus that occurred in the Pliocene and Pleistocene epochs. We propose a scenario for the diversification of Costus, in which rapid floral adaptation in geographic isolation and range shifts in response to environmental changes contribute to reproductive isolation among close relatives. We suggest that these processes may be common in other recently diversified plant lineages centered in Central America or the Northern Andean phytogeographic region.     

基于线粒体COI基因的大蚊属Tipula系统发育及长角大蚊亚属Tipula (Sivatipula)分类地位初步研究(双翅目:大蚊总科)

大蚊属Tipula Linnaeus,1758是大蚊科中种类最多的属,目前其单系性尚未得到全面验证.此外,长角大蚊亚属Tipula (Sivatipula) Alexander,1964因其极长的触角以及独有的精子泵结构,明显不同于大蚊属其他亚属,使其亚属的分类地位存在争议.本研究基于COI序列对19个大蚊属物种及5个其他属物种进行了系统发育分析,并计算了物种间的遗传距离.研究结果表明:(1)邻接树(NJ)和最大似然树(ML)均显示长角大蚊亚属与大蚊属其他亚属未形成单系,大蚊属的单系性没有得到支持;(2)基于遗传距离和系统发育分析并结合形态信息,结果显示长角大蚊亚属独立于大蚊属内其他亚属,应将其提升为属级分类单元.     

A four-gene study of evolutionary relationships in Solanum section Acanthophora

The "spiny solanums," Solanum subgenus Leptostemonum (Solanaceae), comprise a large lineage with over 350 species and include the cultivated eggplant, Solanum melongena. Despite the importance of this subgenus, phylogenetic relationships among these taxa are currently unclear. The present research contributes to this understanding while focusing on Solanum section Acanthophora, a group of ca. 19 species defined by the presence of simple hairs, rather than the stellate hairs common across the rest of subgenus Leptostemonum. In this study we inferred phylogenetic relationships among 29 Solanum taxa, including 14 species of section Acanthophora, using DNA sequence data from two nuclear regions (ITS and the granule-bound starch synthase gene [GBSSI or waxy]) and two chloroplast regions (trnT-trnF and trnS-trnG). This combination of gene regions resulted in a well resolved phylogenetic hypothesis, with results strongly suggesting that Solanum sect. Acanthophora is not monophyletic, although the majority of taxa comprise a monophyletic lineage that is sister to Solanum section Lasiocarpa. Of the four gene regions, waxy was especially useful for phylogenetic inference, with both a high percentage of parsimony-informative sites as well as a low level of homoplasy. Further studies in progress will help elucidate relationships of sect. Acanthophora with respect to other members of subgenus Leptostemonum.     

Phylogenetic analysis of Eremurus,Asphodelus, and Asphodeline (Xanthorrhoeaceae-Asphodeloideae) inferred from plastid trnL-F and nrDNA ITS sequences

The current study represents phylogenetic analyses of Eremurus, Asphodelus and Asphodeline (Xanthorrhoeaceae-Asphodeloideae) using both plastids genome (trnL-F) and the nuclear ribosomal internal transcribed spacer (nrDNA ITS) sequence data. The analyses revealed that each of the investigated genera is monophyletic. Eremurus subgenus Eremurus is monophyletic, whereas the E. subgenus Henningia is paraphyletic. Trachyandra is the closest relative of Eremurus. Bulbinella and Kniphofia are subsequent sisters of Eremurus and Trachyandra. Aloe, Haworthia and Bulbine were nested in a single clade, sister to the last four genera. Asphodeline section Asphodeline appeared to be non-monophyletic, because of the inclusion of A. damascena. All species of Asphodelus analyzed herein, formed a well-supported clade that it is sister to the clade of Asphodeline species.     

Phylogeny of Drosophila and related genera: conflict between molecular and anatomical analyses

Drosophila species are extensively used in biological research; yet, important phylogenetic relationships within the genus and with related genera remain unresolved. The combined data for three genes (Adh, Sod, and Gpdh) statistically resolves outstanding issues. We define the genus Drosophila inclusively so as to include Scaptomyza and Zaprionus (considered distinct genera in the taxonomy of Wheeler, 1981) but excluding Scaptodrosophila. The genus Drosophila so defined is monophyletic. The subgenus Sophophora (including the melanogaster, obscura, and willistoni groups) is monophyletic and the sister clade to all other Drosophila subgenera. The Hawaiian Drosophila (including Scaptomyza) is a monophyletic group, but the subgenus Drosophila is not monophyletic, because the immigrans group is more closely related to the subgenus Hirtodrosophila than to other species of the subgenus Drosophila, such as the virilis and repleta groups.     

Phylogenetic relationships within Plantago (Plantaginaceae): evidence from nuclear ribosomal ITS and plastid trnL-F sequence data

A molecular phylogenetic study of Plantago L. (Plantaginaceae) analysed nucleotide variation in the internal transcribed spacers (ITS) of nuclear ribosomal and plastid trnL-F regions. Included are 57 Plantago species, with two Aragoa species as the ingroup and three Veronica species as the outgroup. Phylogenetic analysis using maximum parsimony identified five major clades, corresponding to the taxonomic groups Plantago subgenera Plantago, Coronopus, Psyllium, Littorella and Bougueria . Aragoa is sister to genus Plantago . Plantago subgenus Littorella is sister to the other subgenera of Plantago . The results are in general correlated with a morphological phylogenetic study and iridoid glucoside patterns, but Plantago subgenus Albicans is paraphyletic and should be included in Plantago subgenus Psyllium sensu lato to obtain a monophyletic clade with six sections. Plantago section Hymenopsyllium is more closely related to section Gnaphaloides than to section Albicans . Plantago subgenus Bougueria is sister to subgenus Psyllium s.l. section Coronopus in Plantago subgenus Coronopus is subdivided in two series. Only some of the sections can be resolved into series. DNA variation within genus Plantago is high, a result that would not have been predicted on the basis of morphology, which is relatively stereotyped. If we calibrate a molecular clock based on the divergence of P. stauntoni , endemic to New Amsterdam in the southern Indian Ocean, we calculate the time of the split between Plantago and Aragoa to be 7.1 million years ago, which is congruent with the fossil record.  © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 139 , 323–338.     

Evolution of a complex coevolved trait: active pollination in a genus of fig wasps

Only three insect lineages have evolved complex active pollination behaviour and only fig wasps (Agaonidae) have also reverted from active to passive pollination. Previously, it was assumed that there was a single origin of active pollination in fig wasps, followed by one independent loss in each of five genera. We show here that there have been three to six changes in pollination behaviour within just one genus (Pleistodontes). The results suggest multiple gains of active pollination in fig wasps, but are sensitive to assumptions about the relative costs of gaining and losing this complex behaviour. In addition, previous comparative studies at higher taxonomic levels have reported correlated evolution between active pollination in wasps and low anther/ovule ratios in figs. We report that changes in pollination behaviour between congeneric species correlate perfectly with changes in anther/ovule ratios in the host figs, showing no phylogenetic inertia in coadaptation at the species level.     

The dominant exploiters of the fig/pollinator mutualism vary across continents,but their costs fall consistently on the male reproductive function of figs

1. Fig trees (Moraceae: Ficus) are keystone species, whose ecosystem function relies on an obligate mutualism with wasps (Chalcidoidea: Agaonidae) that enter fig syconia to pollinate. Each female flower produces one seed (fig female reproductive function), unless it also receives a wasp egg, in which case it supports a wasp. Fig male reproductive function requires both male flowers and pollinator offspring, which are the only vectors of fig pollen. 2. The mutualism is exploited by other wasps that lay eggs but provide no pollination service. Most of these non‐pollinating fig wasps (NPFWs) do not enter syconia, but lay eggs through the wall with long ovipositors. Some are gall‐makers, while others are parasitoids or lethal inquilines of other wasps. 3. Ficus is pan‐tropical and contains >750 fig species. However, NPFW communities vary across fig lineages and continents and their effects on the mutualism may also vary. This provides a series of natural experiments to investigate how the costs to a keystone mutualism vary geographically. 4. We made the first detailed study of the costs of NPFWs in a fig (Ficus obliqua G. Forst) from the endemic Australasian section Malvanthera. In contrast to the communities associated with section Americana in the New World, wasps from the subfamily Sycoryctinae (Chalcidoidea: Pteromalidae) dominated this community. 5. These sycoryctine wasps have a negative impact on pollinator offspring numbers, but not on seed production. Consequently, while the NPFW fauna varies greatly at high taxonomic levels across continents, we show that the consistent main effect of locally dominant exploiters of the mutualism is to reduce fig male reproductive function.     

基于部分线粒体DNA序列的疣螈属亚属(有尾目,蝾螈科,疣螈属)系统发育关系

对疣螈属Yaotriton亚属5个已知物种23个个体的mtDNA序列数据(ND2、tRNATrp、tRNAAla、tRNAAsn、tRNACys和tRNA Tyr,1421bp),使用贝叶斯(BI)和最大似然(M P)方法重建了疣螈属Yaotriton的系统发育关系。结果表明:1)Yaotriton亚属的所有物种形成1个单元群;2)海南疣螈T.hainanensis是Yaotriton亚属的1有效物种,不是细痣疣螈T.asperrimus的同物异名;3)文县疣螈T.wenxianensis雷山种群应是细痣疣螈的地理种群,细痣疣螈绥阳种群应是文县疣螈的地理种群;4)6个文县疣螈地理种群和3个细痣疣螈地理种群分别形成单系群,文县疣螈是Yaotriton亚属的1有效物种。