A survey for biochemical synapomorphies to reveal phylogenetic relationships of halichondrid demosponges (Metazoa: Porifera)

Biochemical compounds are a suggested alternative for morphological characters in sponge systematics. The monophyly of the crucial demosponge order Halichondrida is still largely unresolved. Here, we performed a search for synapomorphies, which might aid to define the order and its five families Axinellidae, Bubaridae, Dictyonellidae, Desmoxyidae and Halichondriidae. We also investigated possible links of the order Halichondrida with other demosponge taxa such as suberitids (Hadromerida). Our survey of published compounds revealed hydroxy-nor-sterols as a potential synapomorphy for axinellid taxa, 2,3,6 sulfated sterol nuclei as possible connection between Agelasida and Halichondrida, besides the known pyrrol-2-carboxylic acids and galactosylceramides, furthermore carbonimidic dichlorides, pupukeananes, diterpene isocyanides for the order Halichondrida and linear and cyclic diterpenes for the family Desmoxyidae. The suitability of biochemical characters in systematics is discussed.     

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).     

A phylogenetic analysis of higher-level gall wasp relationships (Hymenoptera: Cynipidae)

We present the most comprehensive analysis of higher-level relationships in gall wasps conducted thus far. The analysis was based on detailed study of the skeletal morphology of adults, resulting in 164 phylogenetically informative characters, complemented with a few biological characters. Thirty-seven cynipid species from thirty-one genera, including four genera of the apparently monophyletic Cynipini and almost all of the genera in the other tribes, were examined. The outgroup included exemplar species from three successively more distant cynipoid families: Figitidae (the sister group of the Cynipidae), Liopteridae and Ibaliidae. There was considerable homoplasy in the data, but many groupings in the shortest tree were nonetheless well supported, as indicated by bootstrap proportions and decay indices. Partitioning of the data suggested that the high level of homoplasy is characteristic of the Cynipidae and not the result of the amount of available phylogenetically conservative characters being exhausted. The analysis supported the monophyly of the Cynipini (oak gall wasps) which, together with the Rhoditini (the rose gall wasps), Eschatocerini and Pediaspidini formed a larger monophyletic group of gall inducers restricted to woody representatives of the eudicot subclass Rosidae. The inquilines (Synergini) were indicated to be monophyletic, whereas the Aylacini, primarily herb gall inducers, appeared as a paraphyletic assemblage of basal cynipid groups. The shortest tree suggests that the Cynipidae can be divided into three major lineages: one including the inquilines, the Aylacini genera associated with Rosaceae, and Liposthenes ; one consisting entirely of Aylacini genera, among them Aulacidea , Isocolus and Neaylax ; and one comprising the woody rosid gallers (the oak and rose gall wasps and allies), the Phanacis-Timaspis complex and the Aylacini genera associated with Papaveraceae.     

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.     

The phylogenetic relationships among some Randia (Rubiaceae) taxa

Phylogenetic relationships among some Randia (Rubiaceae, Gardenieae) taxa were estimated based on sequence variation in the nuclear ribosomal internal transcribed spacers (ITS) and rps 16 intron (cpDNA). During the investigation of rpsl6 intron of 9 studied Central American Randia species, two well supported subclades were separated. Analysis of ITS data of 16 Randia species shows 3 major clades. A group of mainly lowland, South American Randia species is moderate supported (75%). Species from Mexico form a strongly supported (97%) clade, but the Central American and Mexican Randia species are low supported (58%). However the last two groups are well supported together (95%). The molecular delimination is well in line with the size of leaves combined with the texture of exocarp.     

The phylogenetic relationships and generic limits of finches (Fringillidae)

Phylogenetic relationships among the true finches (Fringillidae) have been confounded by the recurrence of similar plumage patterns and use of similar feeding niches. Using a dense taxon sampling and a combination of nuclear and mitochondrial sequences we reconstructed a well resolved and strongly supported phylogenetic hypothesis for this family. We identified three well supported, subfamily level clades: the Holoarctic genus Fringilla (subfamly Fringillinae), the Neotropical Euphonia and Chlorophonia (subfamily Euphoniinae), and the more widespread subfamily Carduelinae for the remaining taxa. Although usually separated in a different family-group taxon (Drepanidinae), the Hawaiian honeycreepers are deeply nested within the Carduelinae and sister to a group of Asian Carpodacus. Other new relationships recovered by this analysis include the placement of the extinct Chaunoproctus ferreorostris as sister to some Asian Carpodacus, a clade combining greenfinches (Carduelis chloris and allies), Rhodospiza and Rhynchostruthus, and a well-supported clade with the aberrant Callacanthis and Pyrrhoplectes together with Carpodacus rubescens. Although part of the large Carduelis-Serinus complex, the poorly known Serinus estherae forms a distinct lineage without close relatives. The traditionally delimited genera Carduelis, Serinus, Carpodacus, Pinicola and Euphonia are polyphyletic or paraphyletic. Based on our results we propose a revised generic classification of finches and describe a new monotypic genus for Carpodacus rubescens.     

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.     

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.     

Refuting phylogenetic relationships

Background  

Phylogenetic methods are philosophically grounded, and so can be philosophically biased in ways that limit explanatory power. This constitutes an important methodologic dimension not often taken into account. Here we address this dimension in the context of concatenation approaches to phylogeny.     

Molecular analysis of phylogenetic relationships among Myrmecophytic macaranga species (Euphorbiaceae)

Many species of the paleotropical pioneer tree genus Macaranga Thou. (Euphorbiaceae) live in association with ants. Various types of mutualistic interactions exist, ranging from the attraction of unspecific ant visitors to obligate myrmecophytism. In the latter, nesting space and food bodies are exchanged for protection by highly specific ant partners (mainly species of the myrmicine genus Crematogaster). As a first step toward elucidating the coevolution of ant-plant interactions in the Macaranga-Crematogaster system, we have initiated a molecular investigation of the plant partners' phylogeny. Nuclear ribosomal DNA internal transcribed spacer (ITS) sequences were analyzed for 73 accessions from 47 Macaranga species, representing 17 sections or informally described species groups. Three accessions from the putative sister taxon Mallotus Lour, were included as outgroups. Cladograms of the ITS data revealed Macaranga to be nested within Mallotus. ITS sequences are highly similar within section Pachystemon s.str., suggesting a relatively recent and rapid radiation of obligate myrmecophytes within this section. Forty-three accessions, mainly of ant-inhabited species, were additionally investigated by random amplified polymorphic DNA (RAPD) and microsatellite-primed PCR (MP-PCR) techniques. Phenetic analysis of RAPD and MP-PCR banding profiles generally confirmed the ITS results. Best resolutions for individual clades were obtained when ITS and RAPD/MP-PCR data were combined into a single matrix and analyzed phenetically. The combined analysis suggests multiple (four) rather than a single evolutionary origin of myrmecophytism, at least one reversal from obligate myrmecophytism to nonmyrmecophytism, and one loss of mutualistic specifity.     

Genetic constitution and phylogenetic relationships of Japanese crucian carps (Carassius)

The genetic constitution and phylogenetic relationships among the proposed species and subspecies of the crucian carp complex in Japan (Carassius cuvieri, C. auratus subspp. 1 and 2, C. a. grandoculis, C. a. buergeri, and C. a. langsdorfii) were investigated based on analyses of the partial nucleotide sequences of the mitochondrial DNA control region and amplified fragment length polymorphisms of nuclear DNA. Our results demonstrate that C. cuvieri and C. auratus are different entities. However, although several distinct lineages were observed for C. auratus, none corresponded to the proposed subspecies. Moreover, the five subspecies of C. auratus were not necessarily separated genetically from each other. Triploid fish, which are currently classified as a single subspecies (C. a. langsdorfii) but are sometimes treated as an independent species, fell into various clades along with diploid individuals of other subspecies that have the same or similar mitochondrial haplotypes. This suggests that gynogenetic triploid crucian carps distributed throughout the Japanese Archipelago have polyphyletic maternal origins. Our results indicate that Japanese crucian carps are a much more complex assemblage than previously believed.     

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.     

Ancient phylogenetic relationships

Traditional views on deep evolutionary events have been seriously challenged over the last few years, following the identification of major pitfalls affecting molecular phylogeny reconstruction. Here we describe the principally encountered artifacts, notably long branch attraction, and their causes (i.e., difference in evolutionary rates, mutational saturation, compositional biases). Additional difficulties due to phenomena of biological nature (i.e., lateral gene transfer, recombination, hidden paralogy) are also discussed. Moreover, contrary to common beliefs, we show that the use of rare genomic events can also be misleading and should be treated with the same caution as standard molecular phylogeny. The universal tree of life, as described in most textbooks, is partly affected by tree reconstruction artifacts, e.g. (i) the bacterial rooting of the universal tree of life; (ii) the early emergence of amitochondriate lineages in eukaryotic phylogenies; and (iii) the position of hyperthermophilic taxa in bacterial phylogenies. We present an alternative view of this tree, based on recent evidence obtained from reanalyses of ancient data sets and from novel analyses of large combination of genes.     

Reconstruction of phylogenetic relationships

In this paper, we provide an introductory overview to the field of phylogenetic analysis, which has wide applications in modern biology.     

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.     

A multilocus perspective on phylogenetic relationships in the Namib darkling beetle genus Onymacris (Tenebrionidae)

Tenebrionid beetles, common constituent faunae of arid ecosystems worldwide, are particularly abundant in Africa’s Namib and Kalahari deserts. Within this region, flightless, diurnal members of the tribe Adesmiini are among the more intensively studied of all desert beetles, especially with regard to ecology. Much of this research centers on Onymacris, a psammophilous genus largely endemic to the Namib. Here we present the first molecular phylogenetic analysis conducted for Onymacris, emphasizing relationships among other adesmiines. Our multilocus phylogeny identifies a strongly supported clade containing Onymacris and two other genera, Eustolopus and Physadesmia—an assemblage recovered in earlier morphological analyses. However, Onymacris is not monophyletic; rather, we demonstrate its paraphyly with respect to the genus Physadesmia, identified as the sister taxon to the white-bodied species of Onymacris. In turn, the Physadesmia-‘white’ Onymacris clade is the sister group to the remaining (black-bodied) Onymacris. Non-monophyly of ‘black’ versus ‘white’ Onymacris is corroborated by distribution patterns and nodal age estimates, which suggest separate origins in different dune systems.     

Isozyme variation and phylogenetic relationships in Vicia subgenus Cracca (Fabaceae)

BACKGROUND AND AIMS: The phylogenetic relationships among 27 vetch species belonging to the subgenus Cracca of the genus Vicia were studied in comparison with three species of Lathyrus section Lathyrus on the basis of isozyme variation. METHODS: Isozymes encoded by 15 putative loci of ten enzymes were resolved by polyacrylamide gel electrophoresis and isozyme variation was analysed by using parsimony and neighbour-joining methods. KEY RESULTS: The analyses revealed 63 parsimony-informative and 36 species-specific orthozymes. Of the latter, 23 are monomophic and are suitable for identification of V. benghalensis, V. palaestina, V. dumetorum, V. pisiformis, V. sylvatica, V. onobrychioides, V. cappadocica, V. cretica, V. articulata, V. tetrasperma, V. ervilia, V. hirsuta and V. loiseleurii. Polymorphism with heterozygous and homozygous isozyme genotypes was found for V. cracca, V. tenuifolia, V. ochroleuca, V. villosa, V. sylvatica, V. cassubica, V. sparsiflora, V. megalotropis, V. altissima, V. onobrychioides, V. cassia, V. cretica and L. heterophyllus, reflecting outcrossing in these species. By contrast, V. benghalensis, V. palaestina, V. disperma, V. dumetorum, V. pisiformis, V. orobus, V. pauciflora, V. tetrasperma and V. loiseleurii had only homozygous isozyme genotypes at polymorphic loci. Isozyme-based phylogenetic trees are presented. CONCLUSIONS: Sections Cracca, Ervum, Pedunculatae and Lenticula of traditional taxonomy are monophyletic groups, whereas sections Oroboideae (= Vicilla) and Panduratae appear polyphyletic and section Cassubicae is split into two species-couples linked at a low level of support. Treatment of ervoid species in a separate subgenus Ervum is not supported because of its polyphyly.     

Distribution and phylogenetic relationships of Australian glow-worms Arachnocampa (Diptera, Keroplatidae)

Glow-worms are bioluminescent fly larvae (Order Diptera, genus Arachnocampa) found only in Australia and New Zealand. Their core habitat is rainforest gullies and wet caves. Eight species are present in Australia; five of them have been recently described. The geographic distribution of species in Australia encompasses the montane regions of the eastern Australian coastline from the Wet Tropics region of northern Queensland to the cool temperate and montane rainforests of southern Australia and Tasmania. Phylogenetic trees based upon partial sequences of the mitochondrial genes cytochrome oxidase II and 16S mtDNA show that populations tend to be clustered into allopatric geographic groups showing overall concordance with the known species distributions. The deepest division is between the cool-adapted southern subgenus, Lucifera, and the more widespread subgenus, Campara. Lucifera comprises the sister groups, A. tasmaniensis, from Tasmania and the newly described species, A. buffaloensis, found in a high-altitude cave at Mt Buffalo in the Australian Alps in Victoria. The remaining Australian glow-worms in subgenus Campara are distributed in a swathe of geographic clusters that extend from the Wet Tropics in northern Queensland to the temperate forests of southern Victoria. Samples from caves and rainforests within any one geographic location tended to cluster together within a clade. We suggest that the morphological differences between hypogean (cave) and epigean (surface) glow-worm larvae are facultative adaptations to local microclimatic conditions rather than due to the presence of cryptic species in caves.     

Intraspecific variability and phylogenetic relationships of the Pleistocene shrewSorex runtonensis (Soricidae)

Intraspecific variability of the Pleistocene speciesSorex runtonensis Hinton, 1911 from different Polish and Russian (Caucasus Mts.) localities and its relationships to Recent red-toothed shrews of similar body size and mandibular morphology,S. caecutiens Laxmann, 1788 andS. tundrensis Merriam, 1990, are explained on the grounds of multivariate statistics. The remains ofS. runtonensis from different localities form a single group and differ fromS. caecutiens. They resembleS. tundrensis by the first canonical root related to a mandibular size and proportions. This may indicate thatS. runtonensis andS. tundrensis are closely related but separated components of the species complextundrensis.