厕蝇科系统学研究历史与现状

厕蝇科Fanniidae隶属于双翅目Diptera环裂亚目Cyclorrhapha,迄今全世界已知300余种。文章综述厕蝇科昆虫的世界研究简史,列出了200多年来厕蝇分类阶元、分类系统的组合、变动情况,总结该科属下分种团、系统发育、生物地理学研究及我国厕蝇的研究历程。在上述基础上,提出了目前所存在的问题。     

Chromosomes of the Lemuridae

Chromosome studies have been made from skin cultures of 23 individual lemurs representing five different species and including Cheirogaleus medius of the Cheirogaleinae. The results are presented in tabular form and are compared with data from other studies. A detailed study of the chromosomes and replication patterns of L. variegatus ruber and L. v. s. did not reveal any distinguishing features between these subspecies.     

Phylogeny of the Lemuridae: Effects of Character and Taxon Sampling on Resolution of Species Relationships within Eulemur

DNA sequences from three mitochondrial genes and one nuclear gene were analyzed to determine the phylogeny of the Malagasy primate family Lemuridae. Whether analyzed separately or in combination, the data consistently indicate that Eulemur species comprise a clade that is sister to a Lemur catta plus Hapalemur clade. The genus Varecia is basal to both. Resolution of cladogenic events within Eulemur was found to be extremely problematic with a total of six alternative arrangements offered by various data sets and weighting regimes. We attempt to determine the best arrangement of Eulemur taxa through a variety of character and taxon sampling strategies. Because our study includes all but one Eulemur species, increased taxon sampling is probably not an option for enhancing phylogenetic accuracy. We find, however, that the combined genetic data set is more robust to changes in taxon sample than are any of the individual data sets, suggesting that increased character sampling stabilizes phylogenetic resolution. Nonetheless, due to the difficult nature of the problem, we may have to accept certain aspects of Eulemur interrelationships as uncertain.     

Chromosome variability in the Lemuridae

Chromosome studies have been conducted in Lemur catta, L. macaco, L. mongoz, L. fulvus fulvus, and a hybrid L. fulvus fulvus x L. fulvus albifrons. Comparative analysis shows that inter- and intraspecific chromosome variability is a common finding in Lemurs. The Lemuridae are divided into three groups according to the characteristics of their chromosome complement. A reclassification of L. catta with the Hapalemurs is suggested, based on chromosomal and nonchromosomal data.     

Highly repeated DNA analysis and systematics of the Lemuridae,a family of Malagasy prosimians

Hybridization of highly repeated DNA sequences ofEulemur fulvus mayottensis, Lemur catta, andVarecia has been performed on blots of different species of Lemuridae (L. catta, Hapalemur griseus, Varecia variegata variegata, V. v. rubra, E. macaco macaco, E. coronatus, E. mongoz, andE. rubriventer). The probe ofE. fulvus only hybridized with the differentEulemur species, whereas that ofVarecia hybridized with the two subspecies ofVarecia and that ofL. catta with bothL. catta andHapalemur. These results were used to confirm the classification ofVarecia in a separate genus and to review the separation of theL. catta/Hapalemur group from the other species ofEulemur. Comparison of the migration patterns from DNA fragments of these different species has been used to propose a cladogram of the differentEulemur species.     

Phylogeny of the Madagascan endemic family Didiereaceae

A molecular phylogeny of the Didiereaceae was produced through parsimony analysis of chloroplastrpl16 intron andtrnL-trnF andtrnT-trnL intergenic spacer sequences of all eleven species of the Didiereaceae and several outgroup taxa from the Portulacaceae. Results indicated that: 1) the Didiereaceae were embedded within the Portulacaceae, withCalyptrotheca as the sister group of the family; 2) present generic limits were supported; 3)Alluaudiopsis was the most basal lineage; 4) at least two separate episodes of polyploidization within the genusAlluaudia had occurred, and 5) unusually low amounts of variation were present in rapidly evolving noncoding plastid sequences.     

Phylogeny and biogeography of the carnivorous plant family Sarraceniaceae

The carnivorous plant family Sarraceniaceae comprises three genera of wetland-inhabiting pitcher plants: Darlingtonia in the northwestern United States, Sarracenia in eastern North America, and Heliamphora in northern South America. Hypotheses concerning the biogeographic history leading to this unusual disjunct distribution are controversial, in part because genus- and species-level phylogenies have not been clearly resolved. Here, we present a robust, species-rich phylogeny of Sarraceniaceae based on seven mitochondrial, nuclear, and plastid loci, which we use to illuminate this family's phylogenetic and biogeographic history. The family and genera are monophyletic: Darlingtonia is sister to a clade consisting of Heliamphora+Sarracenia. Within Sarracenia, two clades were strongly supported: one consisting of S. purpurea, its subspecies, and S. rosea; the other consisting of nine species endemic to the southeastern United States. Divergence time estimates revealed that stem group Sarraceniaceae likely originated in South America 44-53 million years ago (Mya) (highest posterior density [HPD] estimate = 47 Mya). By 25-44 (HPD = 35) Mya, crown-group Sarraceniaceae appears to have been widespread across North and South America, and Darlingtonia (western North America) had diverged from Heliamphora+Sarracenia (eastern North America+South America). This disjunction and apparent range contraction is consistent with late Eocene cooling and aridification, which may have severed the continuity of Sarraceniaceae across much of North America. Sarracenia and Heliamphora subsequently diverged in the late Oligocene, 14-32 (HPD = 23) Mya, perhaps when direct overland continuity between North and South America became reduced. Initial diversification of South American Heliamphora began at least 8 Mya, but diversification of Sarracenia was more recent (2-7, HPD = 4 Mya); the bulk of southeastern United States Sarracenia originated co-incident with Pleistocene glaciation, <3 Mya. Overall, these results suggest climatic change at different temporal and spatial scales in part shaped the distribution and diversity of this carnivorous plant clade.     

Phylogeny and evolution of the major intrinsic protein family

BACKGROUND INFORMATION: MIPs (major intrinsic proteins) form channels across biological membranes that control recruitment of water and small solutes such as glycerol and urea in all living organisms. Because of their widespread occurrence and large number, MIPs are a sound model system to understand evolutionary mechanisms underlying the generation of protein structural and functional diversity. With the recent increase in genomic projects, there is a considerable increase in the quantity and taxonomic range of MIPs in molecular databases. RESULTS: In the present study, I compiled more than 450 non-redundant amino acid sequences of MIPs from NCBI databases. Phylogenetic analyses using Bayesian inference reconstructed a statistically robust tree that allowed the classification of members of the family into two main evolutionary groups, the GLPs (glycerol-uptake facilitators or aquaglyceroporins) and the water transport channels or AQPs (aquaporins). Separate phylogenetic analyses of each of the MIP subfamilies were performed to determine the main groups of orthology. In addition, comparative sequence analyses were conducted to identify conserved signatures in the MIP molecule. CONCLUSIONS: The earliest and major gene duplication event in the history of the MIP family led to its main functional split into GLPs and AQPs. GLPs show typically one single copy in microbes (eubacteria, archaea and fungi), up to four paralogues in vertebrates and they are absent from plants. AQPs are usually single in microbes and show their greatest numbers and diversity in angiosperms and vertebrates. Functional recruitment of NOD26-like intrinsic proteins to glycerol transport due to the absence of GLPs in plants was highly supported. Acquisition of other MIP functions such as permeability to ammonia, arsenite or CO2 is restricted to particular MIP paralogues. Up to eight fairly conserved boxes were inferred in the primary sequence of the MIP molecule. All of them mapped on to one side of the channel except the conserved glycine residues from helices 2 and 5 that were found in the opposite side.     

Phylogeny and domain evolution in the APETALA2-like gene family

The combined processes of gene duplication, nucleotide substitution, domain duplication, and intron/exon shuffling can generate a complex set of related genes that may differ substantially in their expression patterns and functions. The APETALA2-like (AP2-like) gene family exhibits patterns of both gene and domain duplication, coupled with changes in sequence, exon arrangement, and expression. In angiosperms, these genes perform an array of functions including the establishment of the floral meristem, the specification of floral organ identity, the regulation of floral homeotic gene expression, the regulation of ovule development, and the growth of floral organs. To determine patterns of gene diversification, we conducted a series of broad phylogenetic analyses of AP2-like sequences from green plants. These studies indicate that the AP2 domain was duplicated prior to the divergence of the two major lineages of AP2-like genes, euAP2 and AINTEGUMENTA (ANT). Structural features of the AP2-like genes as well as phylogenetic analyses of nucleotide and amino acid (aa) sequences of the AP2-like gene family support the presence of the two major lineages. The ANT lineage is supported by a 10-aa insertion in the AP2-R1 domain and a 1-aa insertion in the AP2-R2 domain, relative to all other members of the AP2-like family. MicroRNA172-binding sequences, the function of which has been studied in some of the AP2-like genes in Arabidopsis, are restricted to the euAP2 lineage. Within the ANT lineage, the euANT lineage is characterized by four conserved motifs: one in the 10-aa insertion in the AP2-R1 domain (euANT1) and three in the predomain region (euANT2, euANT3, and euANT4). Our expression studies show that the euAP2 homologue from Amborella trichopoda, the putative sister to all other angiosperms, is expressed in all floral organs as well as leaves.     

Phylogeny and character evolution in the bee-assassins (Insecta: Heteroptera: Reduviidae)

Apiomerus, the charismatic bee-assassins (>108 spp.), belong to the New World resin bugs in the harpactorine tribe Apiomerini (12 extant genera) that is characterized by a novel predation strategy, resin trap predation. Apiomerini also exhibit striking genitalic diversity that has shaped subgeneric classifications within the genus Apiomerus and females of some species of Apiomerus are known to engage in unique maternal care behaviors. The lack of a phylogenetic framework currently hinders evolutionary interpretations of genitalic morphology and maternal care. We here present a molecular phylogeny based on 4, 477 bp of six ribosomal and protein coding genes and 95 terminal taxa using parsimony and maximum likelihood approaches as a way of addressing these shortcomings. Apiomerini are monophyletic, with Heniartes being the sistergroup to all remaining taxa that form the monophyletic Manicocoris (Calliclopius, Manicocoris, Micrauchenus, and Ponerobia) and Apiomerus (Agriocoris, Apiomerus, and Sphodrolestes) clades. Previously proposed subgeneric groups are polyphyletic, but several proposed species groups are recovered as monophyletic. Ancestral state reconstruction of the metatibial comb indicates that this structure evolved in the ancestor of all Apiomerini where it was present in males and in females; it became strongly sexually dimorphic (better developed in females than in males) in the Apiomerus clade (Apiomerus + Agriocoris + Sphodrolestes). Genitalic features reveal a pattern of homoplasy, but frequently are nonetheless useful to diagnose supraspecific groups within Apiomerus. The complex genitalia found within Apiomerus are derived for that clade. We conclude that, using the metatibial comb as a proxy, maternal care is relatively common in the tribe Apiomerini and propose that it likely evolved at the base of the Apiomerus clade if not at the base of Apiomerini.     

Phylogeny and character evolution in the Indo-Pacific genus Ctenogobiops (Gobiiformes: Gobiidae)

Ctenogobiops is a genus of Indo-Pacific gobies that form obligate, mutualistic associations with shrimp in the genus Alpheus. This study provides a molecular phylogenetic analysis of eight Ctenogobiops species: C. aurocingulus, C. crocineus, C. feroculus, C. formosa, C. maculosus, C. mitodes, C. tangaroai, and C. tongaensis. We recover two clades within the genus, one consisting of C. feroculus and C. aurocingulus, the second including the remaining species arrayed as follows: (C. tongaensis (C. mitodes (C. formosa (C. maculosus (C. crocineus, C. tangaroai))))). Recovery of C. maculosus and C. crocineus as distinct taxa suggests that these species are not synonymous, although sampling in this study is limited. Species of Ctenogobiops are morphologically very similar to each other, with generally consistent meristic character states present throughout the genus. Recognition of species is based primarily on slight variations in color pattern, shape of the dorsal fin, and size of the gill opening. Comparison of our specimens of C. mitodes with accounts of C. pomastictus confirms that color pattern variations and lateral scale counts are more reliable indicators of species identity than relative dorsal fin spine length, particularly for smaller specimens. We evaluate the distribution of morphological characters in the context of the new phylogenetic hypothesis, and provide a summary of distinguishing characters for Ctenogobiops species. In this case, as in other instances of diverse reef-dwelling fish taxa, molecular data are ideal for inferring phylogenetic relationships, whereas morphological data remain the most expedient way to identify species.     

Phylogenetic systematics and character evolution in the angiosperm family Haloragaceae

The poorly known Haloragaceae R. Br. (Saxifragales) are highly diverse in habit (small trees to submerged aquatics) and labile in floral merosity (2-4), both uncommon among the core eudicots. This family has a cosmopolitan distribution, but taxonomic diversity is concentrated in Australia. An explicit phylogenetic approach has not previously been utilized to examine relationships or character evolution in this family. We used molecular evidence from nrDNA ITS and cpDNA trnK and matK regions under both Bayesian and parsimony analyses to address phylogenetic relationships. Combined molecular analyses defined a monophyletic Haloragaceae with the woody genera (Haloragodendron, Glischrocaryon) sister to the rest. Relationships among many genera were well resolved, with genera as currently delimited generally well supported, although there were notable exceptions; a new genus (Trihaloragis) is recognized, and the aquatic genus Meionectes is again distinct from Haloragis. Three new species combinations are also recognized. There are multiple (two or three) origins of the submerged aquatic habit in the family and potentially an intermediate reversal to the terrestrial habit, neither previously demonstrated in a core eudicot family using an explicit phylogenetic hypothesis. Ancestral character analyses suggest two origins of trimerous flowers and multiple reductions to dimerous flowers throughout Haloragaceae.     

Phylogeny and character evolution in the jelly fungi (Tremellomycetes, Basidiomycota, Fungi)

The Tremellomycetes (Agaricomycotina, Basidiomycota, Fungi) are a nutritionally heterogeneous group comprising saprotrophs, animal parasites, and fungicolous species (fungal-inhabiting, including lichen-inhabiting). The relationships of many species, particularly those with a lichenicolous habit, have never been investigated by molecular methods. We present a phylogeny of the Tremellomycetes based on three nuclear DNA ribosomal markers (nSSU, 5.8S and nLSU), representing all main taxonomic groups and life forms, including lichenicolous taxa. The Cystofilobasidiales, Filobasidiales, Holtermanniales, and Tremellales (including the Trichosporonales) are recovered as monophyletic, but this is not the case for the Tremellomycetes. We suggest, however, that the Cystofilobasidiales tentatively continue to be included in the Tremellomycetes. As currently circumscribed, the Filobasidiaceae, Sirobasidiaceae, Syzygosporaceae and Tremellaceae are non-monophyletic. Cuniculitremaceae, Sirobasidiaceae and Tetragoniomycetaceae are nested within Tremellaceae. The lichenicolous species currently included within the Tremellomycetes belong in this group, distributed across the Filobasidiales and Tremellales. Lichen-inhabiting taxa do not form a monophyletic group; they are distributed in several clades and sometimes intermixed with taxa of other nutritional habits. Character state reconstruction indicates that two morphological traits claimed to characterize groups in the Tremellomycetes (the basidium habit and basidium septation) are highly homoplastic. Comparative phylogenetic methods suggest that the transitions between single and catenulate basidia in the Tremellales are consistent with a punctuational model of evolution whereas basidium septation is likely to have evolved under a graduational model in the clade comprising the Holtermanniales, Filobasidiales, and Tremellales.     

Phylogeny of the Pluteaceae (Agaricales, Basidiomycota): taxonomy and character evolution

The phylogeny of the genera traditionally classified in the family Pluteaceae (Agaricales, Basidiomycota) was investigated using molecular data from nuclear ribosomal genes (nSSU, ITS, nLSU) and consequences for taxonomy and character evolution were evaluated. The genus Volvariella is polyphyletic, as most of its representatives fall outside the Pluteoid clade and shows affinities to some hygrophoroid genera (Camarophyllus, Cantharocybe). Volvariella gloiocephala and allies are placed in a different clade, which represents the sister group of Pluteus, and a new generic name, Volvopluteus, is proposed to accommodate these taxa. Characters such as basidiospore size and pileipellis structure can be used to separate Pluteus, Volvariella and Volvopluteus. The genus Pluteus is monophyletic and includes species with partial veil traditionally classified in the genus Chamaeota. The evolution of morphological features used in the infrageneric taxonomy of the genus, such as metuloid cystidia and pileipellis structure, was analyzed. Agreement between the molecular phylogeny and morphological subdivision of Pluteus is, generally speaking, good, though some rearrangements are necessary: (i) species with non-metuloid pleurocystidia and pileipellis as a cutis are placed either in sect. Celluloderma, together with the species characterized by a hymenidermal pipeipellis, or in sect. Pluteus, with the metuloid bearing species; (ii) subdivision of sect. Celluloderma according to the presence/absence of cystidioid elements in the pileipellis is not supported by molecular data.     

Phylogeny, character evolution, and classification of Sapotaceae (Ericales)

We present the first cladistic study of the largely tropical family Sapotaceae based on both morphological and molecular data. The data were analyzed with standard parsimony and parsimony jackknife algorithms using equally and successive weighted characters. Sapotaceae are confirmed to constitute two main evolutionary lineages corresponding to the tribes Isonandreae‐Mimusopeae‐Sideroxyleae and Chrysophylleae‐Omphalocarpeae. The Sideroxyleae are monophyletic, Isonandreae are polyphyletic as presently circumscribed, and as suggested by the analyses, the subtribe Mimusopeae‐Mimusopinae has evolved within the Mimusopeae‐Manilkarinae, which hence is also paraphyletic. Generic limits must be altered within Sideroxyleae with the current members Argania, Nesoluma and Sideroxylon. Argania cannot be maintained at a generic level unless a narrower generic concept is adopted for Sideroxylon. Nesoluma cannot be upheld in a narrow or broad generic concept of Sideroxylon. The large tribe Chrysophylleae circumscribes genera such as Chrysophyllum, Pouteria, Synsepalum, and Xantolis, but the tribe is monophyletic only if the taxa from Omphalocarpeae are also included. Neither Chrysophyllum nor Pouteria are monophyletic in their current definitions. The results indicate that the African taxa of Pouteria are monophyletic and distinguishable from the South American taxa. Resurrection of Planchonella, corresponding to Pouteria section Oligotheca, is proposed. The African genera Synsepalum and Englerophytum form a monophyletic group, but their generic limits are uncertain. Classification of the Asian genus Xantolis is particularly interesting. Morphology alone is indecisive regarding Xantolis relationships, the combined unweighted data of molecules and morphology indicates a sister position to Isonandreae‐Mimusopeae‐Sideroxyleae, whereas molecular data alone, as well as successive weighted combined data point to a sister position to Chrysophylleae‐Omphalocarpeae. An amended subfamily classification is proposed corresponding to the monophyletic groups: Sarcospermatoideae (Sarcosperma), Sapotoideae (Isonandreae‐Mimusopeae‐Sideroxyleae) and Chrysophylloideae (Chrysophylleae‐Omphalocarpeae), where Sapotoideae circumscribes the tribes Sapoteae and Sideroxyleae as well as two or three as yet unnamed lineages. Morphological characters are often highly homoplasious and unambiguous synapomorphies cannot be identified for subfamilies or tribes, which we believe are the reason for the variations seen between different classifications of Sapotaceae. © The Willi Hennig Society 2005.     

Phylogeny,character evolution,and classification of Selaginellaceae(lycophytes)

Selaginella is the largest and most taxonomically complex genus in lycophytes.The fact that over 750 species are currently treated in a single genus makes Selaginellales/Selaginellaceae unique in pteridophytes.Here we assembled a dataset of six existing and newly sampled plastid and nuclear loci with a total of 684 accessions(74% increase of the earlier largest sampling) representing ca.300 species to infer a new phylogeny.The evolution of 10 morphological characters is studied in the new phylog...     

康氏菌科海洋细菌的系统发育与代谢潜能研究进展

康氏菌科(Kangillaceae)是海洋螺杆菌目(Oceanosprillales)下的科级分类单元,包含康氏菌属(Kangiella)、异康氏菌属(Aliikangiella)和Pleionea三个属.在康氏菌属高度精简的基因组中存在异常丰富的胞外蛋白酶编码基因,暗示此类海洋细菌对海洋颗粒有机物中的蛋白质成分降解具...     

Phylogeny of Pyroleae (Ericaceae): implications for character evolution

Pyroleae (Ericaceae) consist of four genera, all of which are distributed widely in temperate coniferous or sometimes deciduous forests of the Northern Hemisphere. To investigate the phylogenetic relationships among these genera and to explore the evolution of the characteristics of the subfamily, we conducted maximum parsimony and Bayesian analyses with nrDNA ITS and three cpDNA intergenic spacers (atpB-rbcL, trnS-trnG and trnL-trnF). The results from cpDNA and combined cpDNA + ITS data sets strongly support the monophyly of Pyroleae as well as a sister relationship between Pyrola and Moneses–Chimaphila, with Orthilia as the basal lineage. The sister-group relationship between Moneses and Chimaphila is supported by a set of synapomorphies, e.g., single flower, colpate pollen, five bundles in the style, straight fruiting pedicel orientation, complete capsule dehiscence, and the basic chromosome number, x = 13. The Moneses–Chimaphila–Pyrola clade is supported by at least one homologous character of pollen in tetrads. Conflicts associated with the phylogenetic position of Orthilia may imply a hybrid origin for it, and therefore further study is needed.