Advances in clarifying the phylogenetic relationships of acacias: Relevance for biological control

Biological control of invasive Australian acacias will benefit from recent advances in resolving the phylogenetic relationships of Acacia s.l. and Acacia s.s. (“Australian acacias”) within the subfamily Mimosoideae. Some of the phytophage taxa associated with Acacia s.s. display fidelity to a derived clade within the genus. This derived clade contains most of the Acacia s.s. species that have become problematic around the world. Phytophages that are demonstrably restricted to species within the derived clade pose essentially no risk to species outside Acacia s.s.. In contrast, prospective agents able to develop on species in the basal lineages of Acacia s.s. would require more-expansive testing because Acacia s.s. is closely related to the Ingeae, and then sequentially to the genera Acaciella, Mariosousa and Senegalia. Importantly, Vachellia is distantly related to Acacia s.s., being nested in basal Mimoseae lineages, and is thus less likely to be at risk than previously envisaged. Elucidation of these trends shows the benefits of having a comprehensive knowledge of the phylogeny of plants and phytophages under consideration for biological control.     

New microsatellite and CAPS-microsatellite markers for clarifying taxonomic and phylogenetic relationships within Origanum L.

Several species in the genus Origanum L. are important among culinary herbs in the world and local markets as raw materials in herb and spices, pharmaceutical and cosmetic industries. Microsatellites also known as simple sequence repeats are routinely being utilized in many plant species. However, the use of microsatellites has still been limited in the genus Origanum due to the scarcity of specific primer pairs. Until recently, there were only 13 microsatellite primer pairs used in two species of Origanum. This study reported 30 primer pairs for development of microsatellite and CAPS-microsatellite markers in 8 different Origanum species. Microsatellite and CAPS-microsatellite markers were utilized to test whether they were useful in species identification and phylogenetic studies in 65 individual samples representing 8 Origanum species. Results indicated that these markers were very useful to clarify taxonomic uncertainties within the genus since some of the markers produced species-specific amplification fashions. Reported DNA markers could be useful in Origanum breeding studies to select desirable chemotypes and tracing adulteration in commercial herbal materials.     

Assessing the relationships between phylogenetic and functional singularities in sharks (Chondrichthyes)

The relationships between diversity and ecosystem functioning have become a major focus of science. A crucial issue is to estimate functional diversity, as it is intended to impact ecosystem dynamics and stability. However, depending on the ecosystem, it may be challenging or even impossible to directly measure ecological functions and thus functional diversity. Phylogenetic diversity was recently under consideration as a proxy for functional diversity. Phylogenetic diversity is indeed supposed to match functional diversity if functions are conservative traits along evolution. However, in case of adaptive radiation and/or evolutive convergence, a mismatch may appear between species phylogenetic and functional singularities. Using highly threatened taxa, sharks, this study aimed to explore the relationships between phylogenetic and functional diversities and singularities. Different statistical computations were used in order to test both methodological issue (phylogenetic reconstruction) and overall a theoretical questioning: the predictive power of phylogeny for function diversity. Despite these several methodological approaches, a mismatch between phylogeny and function was highlighted. This mismatch revealed that (i) functions are apparently nonconservative in shark species, and (ii) phylogenetic singularity is not a proxy for functional singularity. Functions appeared to be not conservative along the evolution of sharks, raising the conservational challenge to identify and protect both phylogenetic and functional singular species. Facing the current rate of species loss, it is indeed of major importance to target phylogenetically singular species to protect genetic diversity and also functionally singular species in order to maintain particular functions within ecosystem.     

Multivariate map representation of phylogenetic relationships: application to tilapiine fish

Distance matrices obtained from allozyme studies on tilapiine fish are analysed by a multivarite approach. A hierarchical clustering procedure facilitated comparison with tree representations. A map-like representation provided information additional to the tree representation. The current belief that Sarotherodon is closer to Oreochromis than to Tilapia is strengthened. But while it may be the link between these genera at the species level, it is not entirely distinct from Oreochromis at the molecular level. Further, Sarotherodon and Oreochromis species may have arisen from Tilapia in several speciation events. Some of the species interrelations agreed with inferences from morphological data, and disagreed with those from a consensus maximum parsimony (MP) tree. It is suggested that both Chromidotilapia guntheri and Tylochromis jentinki are ancestral to diVerent sub-groups of Tilapia , so that inferences from morphological studies and the consensus MP method are both partially correct. The graphical representation also suggests that the Nile tilapia strains in Asia may be derived from Egypt rather than from Ghana. It is advantageous to use the map-like and tree representations together for maximum visual informativeness and inference from the data.     

Molecular phylogenetic relationships of the deep-sea fish genus Coryphaenoides (Gadiformes: Macrouridae) based on mitochondrial DNA

In order to characterize the phylogenetic relationship and deep-sea adaptation process of the deep-sea fish genus Coryphaenoides, the nucleotide sequences of the mitochondrial (mt) 12 S rRNA and COI gene sequences for seven Coryphaenoides species were analyzed. Our molecular phylogenetic tree shows a new arrangement of seven Coryphaenoides species, which form two distinct groups, abyssal and nonabyssal species, and differs from the results of previous taxonomic studies. Using the mutation rate of mitochondrial genes, the divergence time between abyssal and nonabyssal Coryphaenoides was found to be 3.2-7.6 million years ago. Our study suggests that hydraulic pressure plays an important role in the speciation process in the marine environment.     

Chromosome sizes and phylogenetic relationships between serotypes of Actinobacillus pleuropneumoniae

The genome size of Actinobacillus pleuropneumoniae was determined by pulsed field gel electrophoresis of AscI and ApaI digested chromosomal DNA. The genome size of the type strain 4074^T (serotype 1) was determined to be 2404±40 kb. The chromosome sizes for the reference strains of the other serotypes range between 2.3 and 2.4 Mb. The restriction pattern profiles of AscI, ApaI and NheI digested chromosomes showed a high degree of polymorphism among the different serotype reference strains and allowed their discrimination. The analysis of the macrorestriction pattern polymorphism revealed phylogenetic relationships between the different serotype reference strains which reflect to some extent groups of serotypes known to cross-react serologically. In addition, different pulsed fields gel electrophoresis patterns also revealed heterogeneity in the chromosomal structure among different field strains of serotypes 1, 5a, and 5b, while strains of serotype 9 originating from most distant geographical places showed homogeneous ApaI patterns in pulsed field gel electrophoresis.     

Whole-genome comparison clarifies close phylogenetic relationships between the phyla Dictyoglomi and Thermotogae

The anaerobic thermophilic bacterial genus Dictyoglomus is characterized by the ability to produce useful enzymes such as amylase, mannanase, and xylanase. Despite the significance, the phylogenetic position of Dictyoglomus has not yet been clarified, since it exhibits ambiguous phylogenetic positions in a single gene sequence comparison-based analysis. The number of substitutions at the diverging point of Dictyoglomus is insufficient to show the relationships in a single gene comparison-based analysis. Hence, we studied its evolutionary trait based on whole-genome comparison. Both gene content and orthologous protein sequence comparisons indicated that Dictyoglomus is most closely related to the phylum Thermotogae and it forms a monophyletic group with Coprothermobacter proteolyticus (a constituent of the phylum Firmicutes) and Thermotogae. Our findings indicate that C. proteolyticus does not belong to the phylum Firmicutes and that the phylum Dictyoglomi is not closely related to either the phylum Firmicutes or Synergistetes but to the phylum Thermotogae.     

A survey of tricolpate (eudicot) phylogenetic relationships

The phylogenetic structure of the tricolpate clade (or eudicots) is presented through a survey of their major subclades, each of which is briefly characterized. The tricolpate clade was first recognized in 1989 and has received extensive phylogenetic study. Its major subclades, recognized at ordinal and familial ranks, are now apparent. Ordinal and many other suprafamilial clades are briefly diagnosed, i.e., the putative phenotypic synapomorphies for each major clade of tricolpates are listed, and the support for the monophyly of each clade is assessed, mainly through citation of the pertinent molecular phylogenetic literature. The classification of the Angiosperm Phylogeny Group (APG II) expresses the current state of our knowledge of phylogenetic relationships among tricolpates, and many of the major tricolpate clades can be diagnosed morphologically.     

ADH and phylogenetic relationships ofDrosophila lebanonensis (Scaptodrosophila)

Summary Increasing data onDrosophila alcohol dehydrogenase (ADH) sequences have made it possible to calculate the rate of amino acid replacement per year, which is 1.7×10^–9. This value makes this protein suitable for reconstructing phylogenetic relationships within the genus for those species for which no molecular data are available such asScaptodrosophila. The amino acid sequence ofDrosophila lebanonensis is compared to all of the already knownDrosophila ADHs, stressing the unique characteristic features of this protein such as the conservation of an initiating methionine at the N-terminus, the unique replacement of a glycine by an alanine at a very conserved position in the NAD domain of all dehydrogenases, the lack of a slowmigrating peptide, and the total conservation of the maximally hydrophilic peptide. The functional significance of these features is discussed.Although the percent amino acid identity of the ADH molecule inDrosophila decreases as the number of sequences compared increases, the conservation of residue type in terms of size and hydrophobocity for the ADH molecule is shown to be very high throughout the genusDrosophila. The distance matrix and parsimony methods used to establish the phylogenetic relationships ofD. lebanonensis show that the three subgenera,Scaptodrosophila, Drosophila, andSophophora separated at approximately the same time.     

Spermatozoon ultrastructure and phylogenetic relationships in the monogeneans (platyhelminthes)

Justine J.-L., Lambert A. and Mattei X. 1985. Spermatozoon ultrastructure and phylogenetic relationships in the monogeneans (Platyhelminthes). International Journal for Parasitology15: 601–608. New observations reported in this study together with bibliographical data allow comparisons of spermatozoon ultrastructure in 28 genera of monogeneans, belonging to 19 families. The authors propose to compare and classify monogenean spermatozoa using two simple ultrastructural characteristics: (a) the number of axonemes, 1 or 2, (b) the presence or absence of cortical microtubules. These traits make it possible to group monogenean spermatozoa in four patterns. Pattern 1 (2 axonemes plus microtubules) is characteristic of the polyopisthocotyleans (9 families). The three other patterns are found in the monopisthocotyleans. Pattern 2 (2 axonemes without microtubules) is found in the Capsalidae and Dionchidae, which seem closely related, and also in the Udonellidae, Gyrodactylidae and Euzetrema. Pattern 3 (1 axoneme plus 1 altered axoneme plus microtubules) is found in the Monocotylidae and Loimoidae. Pattern 4 (1 axoneme without microtubules) is found in the Amphibdellatidae, Ancyrocephalidae, Calceostomatidae and Diplectanidae. A phylogeny of the monogeneans is drawn from the data of comparative spermatology; this scheme coincides in many points with the phylogeny of Lambert (1980) which was based on the study of chaetotaxy and ciliated cells of the oncomiracidium.     

On the phylogenetic relationships of trogons (Aves, Trogonidae)

Although trogons (Aves, Trogonidae) are well characterized by the possession of heterodactyl feet, their phylogenetic relationships to other extant birds still are only poorly understood. Molecular studies did not show conclusive results and there are amazingly few comparative studies of the anatomy of trogons. Virtually the only hypothesis on trogon relationships that was supported with derived morphological characters is a sister group relationship to alcediniform birds (bee-eaters, kingfishers, and allies), which share a derived morphology of the columella (ear-ossicle) with trogons. However, in this study a very similar columella is reported for the oilbird (Steatornithidae) and additional previously unrecognized derived osteological characters are presented, which are shared by trogons and oilbirds. A numerical cladistic analysis of 28 morphological characters also resulted in monophyly of Trogonidae and Steatornithidae, although the corresponding node was not retained in a bootstrap analysis.     

A re-evaluation of the phylogenetic relationships in the Apidae (Hymenoptera)

ABSTRACT .
The relationships between the four tribes in the bee family Apidae are re-examined. Characteristics of the postgena, presternum, antenna cleaner, arolium, female hind tibia and male genitalia, among others, support the placement of these tribes in three subfamilies: Meliponinae (Meliponini), Apinae (Apini) and Bombinae (Euglossini + Bombini). The Apinae is the sister group of the Bombinae. This tribal arrangement was originally proposed, using different characteristics, by Winston & Michener (1977).     

On the phylogenetic relationships of Vincelestes neuquenianus

This short review paper compares the lower jaw and lower dentition of the small Mesozoic mammal Vincelestes neuquenianus with some other Laurasian and Gondwanan taxa. On this basis a set of 90 characters recognised by recent authors was assembled and used to construct a cladogram. The topology suggests that the early Cretaceous mammal from Patagonia, Vincelestes, is nested within a clade comprising ‘other Gondwanan mammals’, separated from Laurasian taxa. In general, because there is a lack of Mesozoic mammal skulls from Gondwana, meaning that the skull of Vincelestes can only be compared with cranial material from Laurasia, an incomplete understanding of relationships has resulted in earlier studies. The prototribosphenic condition of Vincelestes is supported by the cladistic analysis presented here and permits a number of interesting speculations because it is of later age than Jurassic tribosphenic mammals from Gondwana. It is proposed that the tribosphenic condition may have developed first amongst taxa on Pangea, before the separation of Laurasia and Gondwana.     

Analysis of mitochondrial DNA: Taxonomic and phylogenetic relationships in two fish taxa (Pisces: Mugilidae and Cyprinidae)

To solve some systematic questions as well as to study genetic variability and evolutionary relationships in two groups of fish belonging to the Mugilid (Mugilidae) and Cyprinid (Cyprinidae) families, we have used restriction fragment length polymorphism analysis of mitochondrial DNA (mtDNA) fragments amplified in polymerase chain reaction. The analysis of three mtDNA fragments of 7220 bp total length of six Mugilid species has shown that Mediterranean Liza aurata, L. ramada, L. saliens, and Chelon labrosus form a common cluster, L. aurata and C. labrosus being the closest relatives, whereas L. haematocheilus (syn. C. haematocheilus) of the Sea of Japan forms a sister group to the Mediterranean cluster. It was found that Chelon and Liza genera are paraphyletic, and therefore their division into two genera is unnatural and they should be synonymized. According to priority, Liza species should be ascribed to Chelon genus. Mugil cephalus is the most distant compared to the rest of the species studied. The level of genetic divergence between allopatric samples of M. cephalus from the Sea of Japan and the Mediterranean Sea has proved to be very high—4.5% of nucleotide substitutions. The analysis of four mtDNA fragments of 9340 bp total length of six Cyprinid species has shown that L. waleckii is the most genetically distant. Pseudaspius leptocephalus is a sister group to Tribolodon species. All Tribolodon species form a common cluster with T. sachalinensis as a root. The remaining species form two branches, one of which includes T. nakamurai and T. brandtii, another one combines T. hakonensis and a new form of Tribolodon revealed that is close to T. hakonensis by its mtDNA (2.4% of nucleotide substitutions). This new form might be an independent species. Published in Russian in Biokhimiya, 2007, Vol. 72, No. 12, pp. 1651–1658.     

Relations between chromosomal findings and prognosis in acute nonlymphoblastic leukemia (author's transl)]

In 48 patients with acute non-lymphoblastic leukemia, all of whom had been treated according to the protocol 7421 of the "acute leukemia group B", remission rates and survival times were correlated with the chromosome constitution of bone marrow cells at diagnosis. 45.8% of the patients had only normal metaphases (N-patients), 31.3% had normal and abnormal metaphases (AN-patients), and 22.9% had only abnormal metaphases (AA-patients). Chromosomal findings were unrelated to patients' age. The remission rate of the N-patients was 72.7%, of the AN-patients 60%, and of the AA-patients 36.4%. The respective median survival times were 12.5, 8.5 and 4.0 months. The difference in remission rates and survival times between patients with normal and without normal metaphases was significant. Once a remission had been obtained the prognosis was similar among the 3 groups. The better prognosis of the AA-patients in this study as compared to previous reports might be related to a more effective chemotherapy.     

Gill monogeneans of neotropical cichlid fish: diversity,phylogenetic relationships,and host-parasite cophylogenetic associations

Host-parasite coevolution is one of the main topics of the evolutionary biology of host-parasite associations. The majority of monogeneans parasitizing fish exhibit a high degree of host specificity. As a result, their evolutionary history might be intertwined with that of their fish hosts. The Cichlidae represent a diverse group of secondary freshwater fish with disjunctive distribution. Host-specific dactylogyrid monogeneans commonly parasitize cichlid fish. Their high diversity is associated with the main areas of cichlid distribution, i.e., Neotropical America and Africa. Nevertheless, the parasite fauna of cichlids from Neotropical America is still underexplored. A total of 31 cichlid species were examined for the presence of monogeneans, with 20 of them being parasitized. On these cichlids, 30 monogeneans belonging to the genera Gussevia, Trinidactylus, and Scadicleithrum were identified, 17 of them potentially representing new species for science. Phylogenetic analyses revealed three monophyletic groups of Neotropic cichlid monogeneans. Genus Gussevia was monophyletic, while Sciadicleithrum resulted polyphyletic. Sciedicleithrum from South America and Sciadicleithrum from Mexico represented two divergent lineages. The plesiomorphic Neotropical cichlid host group for dactylogyrid monogeneans was Cichlini, from which the representatives of other Neotropical cichlid tribes were colonised. Cophylogenetic analyses revealed a statistically significant cophylogenetic signal in the investigated host-parasite system, with host switch and duplication representing the main coevolutionary events for monogeneans parasitizing Neotropical cichlids. This scenario is in accordance with previous studies focussed on dactylogyridean monogeneans parasitizing freshwater fish in Europe and Africa.     

The phylogenetic relationships and natural classificition of the Vespoidea (Hymenptera)

Abstract. Phylogenetic relationships of the subfamilies and tribes of the Vespoidea (= Diploptera) are investigated using cladistic methods. A natural classification is proposed, sequencing seven tribes in six subfamilies within the single family Vespidae. Euparagia is the sister-group of the rest of the Vespidae. The Gayellinae and Masarinae are sister-groups, and are reduced in rank to tribes within the subfamily Masarinae. This is the sister-group of the Eumeninae + Stenogastrinae + Polistinae + Vespinae. The Zethinae is a paraphyletic group; both it and the Raphiglossinae are deleted and included in the Eumeninae. The Stenogastrinae is regarded as the sister-group of the Vespinae + Polistinae.     

Morphological variation and phylogenetic relationships in the genus Anginon (Apiaceae)

The variation in habit and morphology of the twelve species of Anginon, a poorly known southern African genus of woody Apiaceae, is discussed and illustrated. The genus Glia is shown to be the obvious outgroup, sharing with Anginon two convincing synapomorphies: 1, the reduction or partial reduction of the laminar part of the leaves, and 2, the heavily cutinized outer walls of the fruit epidermis. Several characters of the internal structure of the fruit, together with other morphological characters, have been analysed by the cladistic method. Our interpretation of character evolution within the genus and a first hypothesis of phylogenetic relationships, showing three distinct infrageneric groups, is presented.