Gall Mite Molecular Phylogeny and its Relationship to the Evolution of Plant Host Specificity

The phylogenetic relationships of all seven known species of Cecidophyopsis mites (Acari: Eriophyidae) with Ribes hosts have been inferred from ribosomal DNA sequences. This analysis found groups of closely related mites. The five gall-forming species, four of which are monophagous and one which has two hosts, were found in two groups. Another group consisted of the two non gall-forming species, one of which has two hosts, while the other is monophagous. The molecular phylogeny of their known Ribes host plants was calculated using the equivalent ribosomal regions as the mites. The structure of the two trees (mites vs hosts) was clearly different, implying that mite speciation did not closely follow speciation events in the plant hosts. Instead, the three groups of Ribes-infesting Cecidophyopsis mites have derived from a common galling ancestor millions of years ago. Each mite group has recently diversified onto different primary hosts. One group of mites has also lost the galling habit. The results have implications for host range changes and the durability of mite-resistance genes in cultivated Ribes.     

Larval habits, host-plant associations, and speciation in nematine sawflies (Hymenoptera: Tenthredinidae)

Adaptive radiations consist of two intertwined processes, diversification of species and diversification of their ecological niches, but it is unclear whether there is a causal link between the processes. In phytophagous insects, ecological diversification mainly involves shifts in host-plant associations and in larval feeding habits (internal or external) on different plant parts, and several observations indicate that speciation is facilitated by host shifts. Data on host use in individual species suggest that internal feeders are less likely to colonize new hosts than external-feeding taxa and, consequently, increases in collective host ranges and species numbers should be slowed down in endophagous lineages. We tested these related hypotheses by using phylogenetic information to reconstruct the evolutionary history of larval resource use in the sawfly subfamily Nematinae, a group of 1000 plus species with a broad range of niches: the subfamily's combined host range includes over 20 plant families, and larvae may feed externally on leaves or needles, or internally, for example, in buds, fruits, leaves, or galls. The results show that: (1) Most internally feeding groups have evolved independently from external-feeding ancestors, but several distinct internal habits have appeared convergently multiple times; (2) Shifts among host taxa are clearly more common than changes in larval habits; (3) The majority of host switches have occurred among phylogenetically close plant groups, but many shifts are manifest among distantly related, ecologically proximate hosts; (4) Although external feeding characteristic of the common ancestor of Nematinae is associated with relatively high rates of host-shifting, internal feeders are very conservative in their host use; (5) In contrast, the effect of endophagy on speciation probabilities is more variable: net speciation rates are lowered in most internal-feeding groups, but a striking exception is found in species that induce galls on Salicaceae. The loose connection between collective host ranges and species diversity provides empirical support for theoretical models suggesting that speciation rates are a function of a complex interplay between "intrinsic" niche width and resource heterogeneity.     

The place of viruses in the "tree of life"

Ribozymal entry into vesicle containing autocatalytically replicating oligopeptides engendered RNA proliferation and enzyme synthesis within units whose RNA genomes derived from ancestors of viroids. There is good reason to consider the coexistence of proto- or spheroplastic forms of ancient prokaryotes and archaeons. Predecessors of extant mycoplasmavirus L3 or archaeal fuselloviruses could induce cell fusions among these entities. The possibility that the first eukaryotic cells arose consequentially to virally mediated fusions of prokaryotic and archaeal proto- or spheroplasts is presented. Retrotransposons and endogenous retroviruses might have emerged in theropod dinosaurs when Aves evolved; and directed the development of syncytiotrophoblasts in the placentae of the first mammals. As viruses coevolved with their hosts descendants of ancient viruses diverged from one another. Certain phenotypical features could connect extant phages and eukaryotic viruses to common ancestors.     

Geographical Distribution of Phacellaria Benth. (Santalaceae) and its Hosts

Based on the geographical distribution of the species of Phacellaria and its host plants in the world,we speculated on the possible time,sites,and migration of the origin of Phacellaria.The host plants of Phacellaria mainly belong to Loranthaceae.Plants of Phacellaria and their hosts are mainly distributed in tropical and subtropical areas.The plants of Phacellaria might have originated from a tropical area in the south of China before the Tertiary.Their ancestors were parasitic on the ancestors of some plants of Loranthaceae by chance during the Tertiary.It possibly took them millions of years to form a sturdy relationship with their hosts.     

Use of biochemical indices in the classification of Sporozoa

The paper presents a survey of literary and author's own data on metabolism of nitric bases, nucleosides and orotic acid in Eimeria, Toxoplasma and Plasmodium. Experimental data on nucleotide content of DNA, fractional content of ribosome RNA, isofermental spectrum of a number of oxidation-reduction enzymes and immunochemical analysis of antigens in various groups of Sporozoa (Eimeria, Toxoplasma and Plasmodium) are given. A possible use of biochemical and immunochemical data for the taxonomy of Sporozoa is suggested.     

Phylogenetic inference from platyhelminth life-cycle stages

Studies of the life cycle stages of digeneans and oncophoreans (= monogeneans and cestodes) indicate that these two groups had separate origins from free-living rhabdocoel-like ancestors and that the original single-host life cycles became 2-host cycles through accidental ingestion, in digeneans by free-swimming adults being ingested by vertebrates, and in cestodes by eggs being ingested by invertebrates. In both lines a third host was incorporated as a means of increasing the efficiency of transfer between hosts, in digeneans between the primary mollusc and the secondary vertebrate, and in cestodes between the secondary (“first intermediate”) host and the primary vertebrate host.     

Phylogenetic characterization and molecular evolution of bacterial endosymbionts in psyllids (Hemiptera: Sternorrhyncha)

Most sternorrhynchan insects harbor endosymbiotic bacteria in specialized cells (bacteriocytes) near the gut which provide essential nutrients for hosts. In lineages investigated so far with molecular methods (aphids, mealybugs, whiteflies), endosymbionts apparently have arisen from independent infections of common host ancestors and co-speciated with their hosts. Some endosymbionts also exhibit putatively negative genetic effects from their symbiotic association. In this study, the identity of endosymbionts in one major sternorrhynchan lineage, psyllids (Psylloidea), was investigated to determine their position in eubacterial phylogeny and their relationship to other sternorrhynchan endosymbionts. Small-subunit ribosomal RNA genes (16S rDNA) from bacteria in three psyllid species (families Psyllidae and Triozidae) were sequenced and incorporated into an alignment including other insect endosymbionts and free-living bacteria. In phylogenetic analysis, all sequences were placed within the gamma subdivision of the Proteobacteria. Three sequences, one from each psyllid species, formed a highly supported monophyletic group whose branching order matched the host phylogeny, and also exhibited accelerated rates of evolution and mutational bias toward A and T nucleotides. These attributes, characteristic of primary (P) bacteriocyte-dwelling endosymbionts, suggested that these sequences were from the putative psyllid P endosymbiont. Two other sequences were placed within the gamma-3 subgroup of Proteobacteria and were hypothesized to be secondary endosymbionts. The analysis also suggested a sister relationship between P endosymbionts of psyllids and whiteflies. Thus, a continuous mutualistic association between bacteria and insects may have existed since the common ancestor of psyllids and whiteflies. Calculations using a universal substitution rate in bacteria corrected for endosymbiont rate acceleration support the idea that this common ancestor was also the ancestor of all Sternorrhyncha. Compared with other P endosymbiont lineages, the genetic consequences of intracellular life for some psyllid endosymbionts have been exaggerated, indicating possible differences in population structures of bacteria and/or hosts.     

Ecological approach to the problem of monophyly of Neodermata (Platyhelminthes)

The ecological scenario of the evolution of main branches of Neodermata is described. The first neodermateans (= promonogeneans) were parasites of the gill lamellae of Paleozoic jawless vertebrates, which were microphagous suspension-feeding animals. The main apomorphic characters of the primary neodermateans are neodermis, cercomer (posterior hooked attachment organ) and swimming infective larva. All subsequent evolution of Neodermata was related with their acquisition new niches in hosts, which were intensively diverging in that time adapting to new food types and conquering new ecological niches. The acquisition of new microhabitats was accompanied by the development of morphological diversity in Neodermata especially in a structure of attachment and genital organs. Trematoda, Cestoda and Polyopisthocotylea comprise specialized evolutionary lineages and Monopisthocotylea is a basal taxon. Polyopisthocotylea is specialized to the blood feeding on fish gills. The common ancestors of the Trematoda and Cestoda inhabited walls of gills and pharyngeal cavities, from where they penetrated the digestive tract. The aspidogastridean multiloculate hold fast appears to be a highly specialized attachment organ of the monogenean ancestor, which inhabited muscular pharyngeal walls of Paleozoic vertebrates. The loss of cercomer hooks probably took place when mollusk-hosts have been involved in the aspidogastridean life cycle. The extinction of many chondrichthiean groups and progress of small plankton fishes (Teleostei) has led to the appearance Digenea. New vertebrate hosts needed a new infestation type and the cercaria appeared. Parthenogenesis has been developed in stages living in mollusks to counterbalance the loss of individuals at two transmission stages in the digenean cycle; this was resulted in a strong specificity to mollusk-host. Evolutionary tendencies of Trematoda and Cestoda show noticeable similarities.     

Carbohydrate‐binding module tribes

At present, 69 families of carbohydrate‐binding modules (CBMs) have been isolated by statistically significant differences in the amino acid sequences (primary structures) of their members, with most members of different families showing little if any homology. On the other hand, members of the same family have primary and tertiary (three‐dimensional) structures that can be computationally aligned, suggesting that they are descended from common protein ancestors. Members of the large majority of CBM families are β‐sandwiches. This raises the question of whether members of different families are descended from distant common ancestors, and therefore are members of the same tribe. We have attacked this problem by attempting to computationally superimpose tertiary structure representatives of each of the 53 CBM families that have members with known tertiary structures. When successful, we have aligned locations of secondary structure elements and determined root mean square deviations and percentages of similarity between adjacent amino acid residues in structures from similar families. Further criteria leading to tribal membership are amino acid chain lengths and bound ligands. These considerations have led us to assign 27 families to nine tribes. Eight of the tribes have members with β‐sandwich structures, while the ninth is composed of structures with β‐trefoils. © 2014 Wiley Periodicals, Inc. Biopolymers 103: 203–214, 2015.     

On the Procercoid Protonephridial Systems of Three Diphyllobothrium Species (Cestoda, Pseudophyllidea) and Janicki's Cercomer Theory

Because the types of hooks are so similar in the oncosphacra/procercoid ef cestodes and in several groups of monogenclic trcmatodes and because the exterior of a procercoid with the hooks in a cercomer is so suggestive of a monogenetic nematode, the development of the procercoids of three Diphyllobothrium species was studied. The intention was to determine whether or not the procercoid protonephridial system would have a developmental stage when its type is similar to, or identical with that type which characterizes the monogeneans. Such a conformity would greatly support the theory of a common origin of monogeneans and ceslodes. However, it has emerged that no similar developmental stage exists. The ontogeny revealed a thorough metamorphosis from a very simple primary protonephridial system (identical with that of the miracidium larva in digeneans) to a secondary system, which develops into the system of the adult tapeworm. This fact may be interpreted as an argument against the supposed inter-relalionships between monogeneans and cestodes. However, the type of hooks and the procercoid cercomer still indicate common ancestors. An analysis of the miracidium, the oncosphaera and the oncomiracidium (the monogenean larva) with reference to their different developmental stages when hatching, gave rise to my interpretation of the fundamental structure of both the miracidium and the oncosphaera as primitively simple and not reduced, Especially the identical type of protonephridial system indicates. in my view, that digeneans and ceslodes originally had a common larva type. If the ceslodes and the monogeneans have common ancestors, then the procercoid may be interpreted as the ontogenetic recapitulation of a common hook-armed ancestor, here named hexucanthoid. This rhabdocoelan creature with six hooks in the cercomer and adapted to an ectocommensalic/ectoparasitic mode of life, is thought to have given rise to the monogeneans, the gyrocotylideans, the amphilinideans and the cestodes. The monogeneans were found to have two fundamentally different types of marginal hooks, and on this basis ihe existence of two different lines of evolution in Monogenea is indicated.     

Evolutionary patterns in life histories of Oxyurida

The Oxyurida comprises some 850 known species that occur in the intestine of arthropods and vertebrates (one species in annelids). Important arthropod hosts include Diplopoda, Blattodea, Gryllotalpoidea, Passalidae, Scarabaeida and Hydrophilidae. The major vertebrate hosts are lizards, tortoises, primates, rodents and lagomorphs. An underlying characteristic of the group is haplodiploid reproduction and like many haplodiploid groups, pinworms tend to have life histories that involve high levels of inbreeding. Unlike Strongylida, Ascaridida and Spirurida, which have diversified in tissue site and life cycle as well as hosts, pinworms show little variation in these features and have radiated only across host groups. Two explanations are advanced for this. Haplodiploidy and its concomitant inbreeding may act to canalise evolutionary change, although diverse groups such as the Hymenoptera belie this. Alternatively, Strongylida, Ascaridida and Spirurida are presumed to have arisen from skin-penetrating ancestors that were forced to undergo a tissue migration before reaching their primitive tissue site, the gut. This migration demanded they adapt to a variety of tissue sites and thus acted as a preadaptation to further diversification. The Oxyurida, in contrast, probably arose using oral contaminative transmission. The lack of exposure to other tissue sites may therefore have relegated pinworms to their position in the posterior gut.     

Distribution of Lambornella clarki (Ciliophora: Tetrahymenidae) and other mosquito parasites in California treeholes

Lambornella clarki (Ciliophora: Tetrahymenidae) was one of three common parasites infecting larvae of Aedes sierrensis (Diptera: Culicidae) in California treeholes sampled between 1983 and 1985. Lambornella occurred in 37 of 142 treeholes and was absent from holes with extremes of pH and high electrical conductivity. Ciliates were more common in treeholes in northern California, and L. clarki from all holes was pathogenic to Ae. sierrensis. Natural infection rates averaged 16.1% but reached 100% in some holes suggesting that epizootics may occur in natural host populations. Sequential sampling of treeholes indicated that free-swimming trophozoites appeared shortly after treeholes flooded, but their numbers declined in subsequent samples. Predation by Ae. sierrensis larvae and successful attack and entry of hosts probably accounted for this decline. Trophozoites were common in treehole water late in the season as adult mosquitoes were emerging, and these were probably released from moribund and dead infected hosts. The parasite persisted in dry treeholes between wet seasons in 90% of the cases indicating a highly efficient desiccation resistant cyst. Octomyomermis troglodytis (Nematoda: Mermithidae) and Ascogregarina clarki (Sporozoa: Eugregarinida) were found in 17 and 46 treeholes, respectively. The cooccurrence of these parasites and L. clarki within treeholes did not deviate from random, indicating that parasites are not segregated among larval habitats. All combinations of parasites were found within individual hosts suggesting that competitive forces in this parasite guild are probably weak.     

Geographical Distribution of Phacellaria Benth. (Santalaceae) and its Hosts

Based on the geographical distribution of the species of Phacellaria and its host plants in the world, we speculated on the possible time, sites, and migration of the origin of Phacellaria. The host plants of Phacellaria mainly belong to Loranthaceae. Plants of Phacellaria and their hosts are mainly distributed in tropical and subtropical areas. The plants of Phacellariamight have originated from a tropical area in the south of China before the Tertiary. Their ancestors were parasitic on the ancestors of some plants of Loranthaceae by chance during the Tertiary. It possibly took them millions of years to form a sturdy relationship with their hosts. Translated from Guihaia, 2005, 25(2) (in Chinese)     

Brachylaima apoplania n. sp. (Digenea: Brachylaimidae) from the Polynesian rat, Rattus exulans (Rodentia: Muridae), in New Zealand: origins and zoogeography

Brachylaima apoplania n. sp. is described from the small intestine of the Polynesian rat (Rattus exulans) on Tiritiri Matangi Island, New Zealand. The new species is most similar to Brachylaima ratti Baugh, 1962, from Rattus rattus. The two species differ only in morphometric characters, B. apoplania possessing significantly smaller suckers, pharynx, testes, ovary, and cirrus sac. The close resemblance between B. apoplania and B. ratti, the close relationship between their hosts, and archaeological evidence on the origin and early dispersal of R. exulans are used to hypothesize a common Southeast Asian origin for the 2 Brachylaima species. Brachylaima apoplania is believed to have dispersed subsequently throughout the South Pacific islands, along with its rodent host, in the canoes of the ancestors of the modern Polynesians and Maoris.     

The time to the ancestor along sequences with recombination.

In a sample of DNA sequences where recombination can occur to the ancestors of the sample, distinct parts of the sequences may have different most recent common ancestors. This paper presents a Markov chain Monte Carlo algorithm for computing the expected time to the most recent common ancestor along the sequences, conditional on where the mutations occur on the sequences.     

The interactions of intracellular Protista and their host cells, with special reference to heterotrophic organisms.

Intracellular genera are found in all the major groups of Protista, but are particularly common among the dinoflagellates, trypanosomatid zooflagellates and suctorian ciliates; the Sporozoa are nearly all intracellular at some stage of their life, and the Microspora entirely so. Intracellular forms can dwell in the nucleus, within phagosomal or other vacuoles or may lie free in the hyaloplasm of their host cells. Organisms tend to select their hosts from a restricted taxonomic range although there are some notable exceptions. There is also great variation in the types of host cell inhabited. There are various reasons for both host and cell selectivity including recognition phenomena at the cell surfaces. Invasion of host cells is usually preceded by surface interactions with the invader. Some organisms depend upon phagocytosis for entry, but others induce host cells to engulf them by non-phagocytic means or invade by microinjection through the host plasma membrane. Protista avoid lysosomal destruction by their resistance to enzyme attack, by surrounding themselves with lysosome-inhibiting vacuoles, by escaping from the phagosomal system into the hyaloplasm and by choosing host cells which lack lysosomes. Nutrition of intracellular heterotrophic organisms involves some degree of competition with the host cell's metabolism as well as erosion of host cell cytoplasm. In Plasmodium infections, red cells are made more permeable to required nutrients by the action of the parasite on the host cell membrane. The parasite is often dependent upon the host cell for complex nutrients which it cannot synthesize for itself. Intracellular forms often profoundly modify the structure and metabolism of the host cell or interfere with its growth and multiplication. This may result in the final lysis of the host cell at the end of the intracellular phase or before the infection of other cells. Certain types of intracellular organisms may have arisen initially as forms attached to the cell surface of digestive or other organs, but the intracellular habit appears to have arisen independently in several groups of Protista.     

Thioesterases: A new perspective based on their primary and tertiary structures

Thioesterases (TEs) are classified into EC 3.1.2.1 through EC 3.1.2.27 based on their activities on different substrates, with many remaining unclassified (EC 3.1.2.–). Analysis of primary and tertiary structures of known TEs casts a new light on this enzyme group. We used strong primary sequence conservation based on experimentally proved proteins as the main criterion, followed by verification with tertiary structure superpositions, mechanisms, and catalytic residue positions, to accurately define TE families. At present, TEs fall into 23 families almost completely unrelated to each other by primary structure. It is assumed that all members of the same family have essentially the same tertiary structure; however, TEs in different families can have markedly different folds and mechanisms. Conversely, the latter sometimes have very similar tertiary structures and catalytic mechanisms despite being only slightly or not at all related by primary structure, indicating that they have common distant ancestors and can be grouped into clans. At present, four clans encompass 12 TE families. The new constantly updated ThYme (Thioester‐active enzYmes) database contains TE primary and tertiary structures, classified into families and clans that are different from those currently found in the literature or in other databases. We review all types of TEs, including those cleaving CoA, ACP, glutathione, and other protein molecules, and we discuss their structures, functions, and mechanisms.     

重寄生属植物及其寄主的地理分布

通过对重寄生属植物及其寄主的地理分布状况的讨论,对重寄生属植物可能的起源时间、地点与迁 移进行了分析。重寄生属植物主要寄生在桑寄生科(Loranthaceae)植物上,重寄生属植物的分布区与其寄主 的基本一致,均主要分布在东南亚和中国南部的热带与亚热带地区;重寄生属植物可能起源于第三纪之前某 一时期的华南热带地区,随后向周边地区扩散。在第三纪,重寄生属植物的祖先偶然寄生在桑寄生科某些寄 生植物祖先上,经过几千万年的协同进化,形成了今天比较稳定的寄生与寄主关系。     

Phylogeny of Ultra-Rapidly Evolving Dinoflagellate Chloroplast Genes: A Possible Common Origin for Sporozoan and Dinoflagellate Plastids

Complete chloroplast 23S rRNA and psbA genes from five peridinin-containing dinoflagellates (Heterocapsa pygmaea, Heterocapsa niei, Heterocapsa rotun-data, Amphidinium carterae, and Protoceratium reticulatum) were amplified by PCR and sequenced; partial sequences were obtained from Thoracosphaera heimii and Scrippsiella trochoidea. Comparison with chloroplast 23S rRNA and psbA genes of other organisms shows that dinoflagellate chloroplast genes are the most divergent and rapidly evolving of all. Quartet puzzling, maximum likelihood, maximum parsimony, neighbor joining, and LogDet trees were constructed. Intersite rate variation and invariant sites were allowed for with quartet puzzling and neighbor joining. All psbA and 23S rRNA trees showed peridinin-containing dinoflagellate chloroplasts as monophyletic. In psbA trees they are related to those of chromists and red algae. In 23S rRNA trees, dinoflagellates are always the sisters of Sporozoa (apicomplexans); maximum likelihood analysis of Heterocapsa triquetra 16S rRNA also groups the dinoflagellate and sporozoan sequences, but the other methods were inconsistent. Thus, dinoflagellate chloroplasts may actually be related to sporozoan plastids, but the possibility of reproducible long-branch artifacts cannot be strongly ruled out. The results for all three genes fit the idea that dinoflagellate chloroplasts originated from red algae by a secondary endosymbiosis, possibly the same one as for chromists and Sporozoa. The marked disagreement between 16S rRNA trees using different phylogenetic algorithms indicates that this is a rather poor molecule for elucidating overall chloroplast phylogeny. We discuss possible reasons why both plastid and mitochondrial genomes of alveolates (Dinozoa, Sporozoa and Ciliophora) have ultra-rapid substitution rates and a proneness to unique genomic rearrangements. Received: 27 December 1999 / Accepted: 24 March 2000     

The skull and jaw musculature as guides to the ancestry of salamanders

The fossil record provides no evidence supporting a unique common ancestry for frogs, salamanders and apodans. The ancestors of the modern orders may have diverged from one another as recently as 250 million years ago, or as long ago as 400 million years according to current theories of various authors. In order to evaluate the evolutionary patterns of the modern orders it is necessary to determine whether their last common ancestor was a rhipidistian fish, a very primitive amphibian, a labyrimhodom or a ‘lissamphibian’. The broad cranial similarities of frogs and salamanders, especially the dominance of the braincase as a supporting element, can be associated with the small size of the skull in their immediate ancestors. Hynobiids show the most primitive cranial pattern known among the living salamander families and “provide a model for determining the nature of the ancestors of the entire order. Features expected in ancestral salamanders include: (1) Emargination of the cheek; (2) Movable suspensorium formed by the quadrate, squamosal and pterygoid; (3) Occipital condyle posterior to jaw articulation; (4) Distinct prootic and opisthotic; (5) Absence ol otic notch; (6) Stapes forming a structural link between braincase and cheek. In the otic region, cheek and jaw suspension, the primitive salamander pattern (resembles most closely the microsaurs among known Paleozoic amphibians, and shows no significant features in common with either ancestral frogs or the majority of labyrinth odonts. The basic pattern of the adductor jaw musculature is consistent within both frogs and salamanders, but major differences are evident between the two groups. The dominance of the adductor mandibulae externus in salamanders can be associated with the open cheek in all members of that order, and the small size of this muscle in frogs can be associated with the large otic notch. The spread of different muscles over the otic capsule, the longus head ol the adductor mandibulae posterior in frogs and the superficial head of the adductor mandibulae internus in salamanders, indicates that fenestration of the skull posterodorsal to the orbit occurred separately in the ancestors of the two groups. Reconstruction of the probable pattern of the jaw musculature in Paleozoic amphibians indicates that frogs and salamanders might have evolved from a condition hypothesized for primitive labyrinthodonts, but the presence of a large otic notch in dissorophids suggests specialization toward the anuran, not the urodele condition. The presence of either an einarginated cheek or an embayment of the lateral surface of the dentary and the absence of an otic notch in microsaurs indicate a salamander-like distribution of die adductor jaw muscles. The ancestors of frogs and salamanders probably diverged from one another in the early Carboniferous, Frogs later evolved from small labyrinthodonts and salamanders from microsaurs. Features considered typical of lissamphibians evolved separately in the two groups in the late Permian andTriassic.