Phylogeny of the genus Hesperodiaptomus (Copepoda) based on nucleotide sequence data of the nuclear ribosomal gene

The genus Hesperodiaptomus Light, 1938, one of the most diverse groups of freshwater copepods that occur in North and Central America, plays a major role in the food webs of the alpine freshwater communities. Phylogenetic relationships of these taxa remain poorly understood due to difficulties in obtaining reliable morphological characters for phylogenetic analyses. To understand the phylogenetic relationships within this group, we reconstructed a partial phylogeny of the genus Hesperodiaptomus based on nuclear ribosomal gene sequences. Phylogenetic analyses based upon the taxa examined supported the monophyly the genus and revealed two clades. The eiseni clade comprised species that are morphologically similar to Hesperodiaptomus eiseni (Lilljeborg, 1889), and the shoshone clade included species morphologically similar to Hesperodiaptomus shoshone (S.A. Forbes, 1882). The two groups can be distinguished by a modification of the right basis, the arrangement of spinules on the distal pad of the second exopod, and the degree of presence the inner lamellar expansion of the right coxa. Handling editor: P. Spaak     

A molecular phylogeny of Planorboidea (Gastropoda, Pulmonata): insights from enhanced taxon sampling

Planorbid gastropods are the most diverse group of limnic pulmonates, with both discoidal and highspired taxa. Phylogenetic relationships among these genera are confused and controversial. In particular, the monophyly of the limpet‐like taxa (traditionally Ancylidae) is disputed. Even recent molecular studies have concluded that substantially more work is necessary to solve the remaining issues concerning intergeneric phylogenetic relationships and higher taxa systematics. Planorbid snails are of great significance for humans as several members of this group are intermediate hosts of blood flukes (schistosomes) causing a chronic disease, schistosomiasis. We used the two independent molecular markers COI and 18S (concatenated dataset of 2837 nucleotide bp) to infer phylogenetic relationships of 26 genera (27 species) of Planorboidea, represented mostly by type species from mainly topotypical populations. With the majority of the taxa discussed not having been studied previously, this study attempted to test several hypotheses on planorbid phylogenetic relationships using Bayesian inference techniques. The monophyly of Planorboidea (= ‘Ancyloplanorbidae’) is strongly suggested on the basis of our extensive molecular analysis. Besides a distinct Burnupia clade, two major clades were recovered that correspond to family level taxa (traditional Bulinidae and Planorbidae). Considerable rearrangements of suprageneric taxa are evident from the phylogeny inferred. Therefore, the only clades recognized by current classifications and supported by our analysis are Planorbini and Segmentinini. The present study found that Ancylidae as traditionally understood, i.e. covering most freshwater limpet gastropods, is paraphyletic, as the genera of Burnupia and Protancylus have been shown to lie phylogenetically outside the Ancylini. Chromosome numbers and levels of polyploidy are discussed in the light of the new phylogeny. An earlier theory of shell shape evolution, i.e. that of patelliform taxa being most advanced, was not supported by this study; a limpet‐shaped taxon is most basal within Planorboidea. Although many taxa still remain to be studied, our results will hopefully contribute towards a better understanding of this very important group of freshwater organisms. Some taxonomic implications are discussed.     

Convergence and parallelism: is a new life ahead of old concepts?

In comparative biology, character observations initially separate similar and dissimilar characters. Only similar characters are considered for phylogeny reconstruction; their homology is attested in a two‐step process, firstly a priori of phylogeny reconstruction by accurate similarity statements, and secondly a posteriori of phylogeny analysis by congruence with other characters. Any pattern of non‐homology is then a homoplasy, commonly, but vaguely, associated with “convergence”. In this logical scheme, there is no way to analyze characters which look similar, but cannot meet usual criteria for homology statements, i.e., false similarity detected a priori of phylogenetic analysis, even though such characters may represent evolutionarily significant patterns of character transformations. Because phylogenies are not only patterns of taxa relationships but also references for evolutionary studies, we propose to redefine the traditional concepts of parallelism and convergence to associate patterns of non‐homology with explicit theoretical contexts: homoplasy is restricted to non‐similarity detected a posteriori of phylogeny analysis and related to parallelism; non‐similarity detected a priori of phylogenetic analysis and necessarily described by different characters would then correspond to a convergence event s. str. We propose to characterize these characters as heterologous (heterology). Heterology and homoplasy correspond to different non‐similarity patterns and processes; they are also associated with different patterns of taxa relationships: homoplasy can occur only in non‐sister group taxa; no such limit exists for heterology. The usefulness of these terms and concepts is illustrated with patterns of acoustic evolution in ensiferan insects. © The Willi Hennig Society 2005.     

Phylogeny of Cyperaceae Based on DNA Sequence Data: Current Progress and Future Prospects

In the last decade, efforts to reconstruct suprageneric phylogeny of the Cyperaceae have intensified. We present an analysis of 262 taxa representing 93 genera in 15 tribes, sequenced for the plastid rbcL and trnL-F (intron and intergenic spacer). Cyperaceae are monophyletic and resolved into two clades, here recognised as Mapanioideae and Cyperoideae, and the overall topology is similar to results from previous studies. Within Cyperoideae, Trilepideae are sister to rest of taxa whereas Cryptangieae, Bisboeckelerieae and Sclerieae are resolved within Schoeneae. Cladium and Rhynchospora (and Pleurostachys) are resolved into clades sister to the rest of Schoeneae, lending support to the recognition of these taxa in separate tribes. However, we retain these taxa in Schoeneae pending broader sampling of the group. The phylogenetic position of 40 species in 21 genera is presented in this study for the first time, elucidating their position in Abildgaardieae (Trachystylis), Cryptangieae (Didymiandrum, Exochogyne), Cypereae (Androtrichum, Volkiella), Eleocharideae (Chillania), and Schoeneae (Calyptrocarya, Morelotia). More sampling effort (more taxa and the use of more rapidly evolving markers) is needed to resolve relationships in Fuireneae and Schoeneae.     

Integrative taxonomy approach for analysing evolutionary history of the tribe Euseiini Chant & McMurtry (Acari: Phytoseiidae)

Phylogenetic relationships within the mite Family Phytoseiidae are little known. The presently accepted classification is based on the opinion of specialists, but not on cladistics analysis. The present paper focuses on the tribe Euseiini, containing 271 species, three subtribes and 10 genera. It aims to determine phylogenetic relationships between these taxa and test their monophyly. Molecular analysis combining six markers has been carried out for taxa we succeeded in collecting. Morphological, biogeographic and ecological data have been analysed to determine how these factors can explain the evolutionary relationships emphasized on the phylogenetic tree. Those analyses have been carried out for the taxa available for the molecular study, but also for all species of the tribe. The tribe Euseiini and the two subtribes considered are monophyletic (at least considering the available taxa), supporting the present hypothesis on Phytoseiidae classification. However, the genus Iphiseius seems to not be valid and its unique species is included in the genus Euseius. Clades that were observed within the genus Euseius do not match with recent work on species groups within this genus. It seems that some morphological features such as an insemination apparatus shape and seta length on the dorsal shield constitute some elements explaining the clusters within the genus Euseius. Biogeographic and ecological data analysis led us to hypothesize a west Gondwanian origin of the tribe Euseiini (Africa and Neotropical areas) on Rosids plants (especially of the Orders Malpiphiales and Fabales: subclass Fabidae). Further analyses are still required to (i) take into account more taxa (especially rare ones and species from the Ethiopian part), (ii) to consider more accurate morphological features through more powerful microscopic apparatus, and (iii) to associate a phylogenetic and evolutionary scenario to life traits (pollen feeders).     

Ecological and Phylogenetic Correlates to Body Size in the Indriidae

I investigated ecological and phylogenetic correlates to body size variations in 10 taxa of extant Indriidae (Indri, Avahi, and Propithecus). I also tested for phylogenetic niche conservatism as a model for the evolution of indriid body size. Phylogenetic niche conservatism refers to the shared attributes that related taxa have acquired because they tend to have occupied similar niches during their evolutionary history. I collected species-specific data on body mass, climate, density, and chemical properties of food items from the literature. I used 2 phylogenies in independent contrasts methods to control for phylogenetic relationships (Indri and Propithecus as sister taxa vs. Indri basal taxa to all indriids). Multivariate models indicated that lemur density and resource quality are the strongest ecological correlates to indriid body size variations. Partitioning methods revealed that 52.4–67% of indriid body size variation is explained by phylogenetic niche conservation. Thus, indriid body size variations may be the result of stabilizing selection. Though it is possible to identify constraints on lower than average body size, there are few data on selection against larger than average body size in indriids. Large body size in subfossil lemurs further complicates identification of constraints on larger than average body size in extant indriids. Researchers using independent contrast methods to control for phylogeny should be aware that some ecology-phenotype relationships are best explained as the result of the synergistic effects of ecology and phylogeny.     

Modeling nucleotide evolution at the mesoscale: the phylogeny of the neotropical pitvipers of the Porthidium group (viperidae: crotalinae)

We analyzed the phylogeny of the Neotropical pitvipers within the Porthidium group (including intra-specific through inter-generic relationships) using 1.4 kb of DNA sequences from two mitochondrial protein-coding genes (ND4 and cyt-b). We investigated how Bayesian Markov chain Monte-Carlo (MCMC) phylogenetic hypotheses based on this 'mesoscale' dataset were affected by analysis under various complex models of nucleotide evolution that partition models across the dataset. We develop an approach, employing three statistics (Akaike weights, Bayes factors, and relative Bayes factors), for examining the performance of complex models in order to identify the best-fit model for data analysis. Our results suggest that: (1) model choice may have important practical effects on phylogenetic conclusions even for mesoscale datasets, (2) the use of a complex partitioned model did not produce widespread increases or decreases in nodal posterior probability support, and (3) most differences in resolution resulting from model choice were concentrated at deeper nodes. Our phylogenetic estimates of relationships among members of the Porthidium group (genera: Atropoides, Cerrophidion, and Porthidium) resolve the monophyly of the three genera. Bayesian MCMC results suggest that Cerrophidion and Porthidium form a clade that is the sister taxon to Atropoides. In addition to resolving the intra-specific relationships among a majority of Porthidium group taxa, our results highlight phylogeographic patterns across Middle and South America and suggest that each of the three genera may harbor undescribed species diversity.     

A mobile element based phylogeny of Old World monkeys

SINEs (Short INterspersed Elements) are a class of non-autonomous mobile elements that are <500 bp in length and have no open reading frames. Individual SINE elements are essentially homoplasy free with known ancestral states, making them useful genetic systems for phylogenetic studies. Alu elements are the most successful SINE in primate genomes and have been utilized for resolving primate phylogenetic relationships and human population genetics. However, no Alu based phylogenetic analysis has yet been performed to resolve relationships among Old World monkeys. Using both a computational approach and polymerase chain reaction display methodology, we identified 285 new Alu insertions from sixteen Old World monkey taxa that were informative at various levels of catarrhine phylogeny. We have utilized these elements along with 12 previously reported loci to construct a phylogenetic tree of the selected taxa. Relationships among all major clades are in general agreement with other molecular and morphological data sets but have stronger statistical support.     

Phylogeny and biogeography of Chinese and Australasian Polystichum ferns as inferred from chloroplast trnL-F and rps4-trnS sequence data

Polystichum, one of the largest genera of ferns, occurs worldwide with the greatest diversity in southwest China and adjacent regions. Although there have been studies of Chinese Polystichum on its traditional classification, geographic distributions, and even a few on its molecular systematics, its relationships to other species outside China remain little known. Here, we investigated the phylogeny and biogeography of the Polystichum species from China and Australasia. The evolutionary relationships among 42 Polystichum species found in China (29 taxa) and Australasia (13 taxa) were inferred from phylogenetic analyses of two chloroplast DNA sequence data sets: rps4-trnS and trnL-F intergenic spacers. The divergence time between Chinese and Australasian Polystichum was estimated. The results indicated that the Australasian species comprise a monophyletic group that is nested within the Chinese diversity, and that the New Zealand species are likewise a monophyletic group nested within the Australasian species. The divergence time estimates suggested that Chinese Polystichum migrated into Australasia from around 40 Ma ago, and from there to New Zealand from about 14 Ma. The diversification of the New Zealand Polystichum species began about 10 Ma. These results indicated that Polystichum probably originated in eastern Asia and migrated into Australasia: first into Australia and then into New Zealand.     

Reconstructing the evolution of agarics from nuclear gene sequences and basidiospore ultrastructure

Traditional classifications of agaric fungi involve gross morphology of their fruit bodies and meiospore print-colour. However, the phylogeny of these fungi and the evolution of their morphological and ecological traits are poorly understood. Phylogenetic analyses have already demonstrated that characters used in traditional classifications of basidiomycetes may be heavily affected by homoplasy, and that non-gilled taxa evolved within the agarics several times. By integrating molecular phylogenetic analyses including domains D1–D3 and D7–D8 of nucLSU rDNA and domains A–C of the RPB1 gene with morphological and chemical data from representative species of 88 genera, we were able to resolve higher groups of agarics. We found that the species with thick-walled and pigmented basidiospores constitute a derived group, and hypothesize that this specific combination of characters represents an evolutionary advantage by increasing the tolerance of the basidiospores to dehydration and solar radiation and so opened up new ecological niches, e.g. the colonization of dung substrates by enabling basidiospores to survive gut passages through herbivores. Our results confirm the validity of basidiospore morphology as a phylogenetic marker in the agarics.     

Molecular phylogeny and evolution of subsection Magnicellulatae (Erysiphaceae: Podosphaera) with special reference to host plants

The subsection Magnicellulatae of the genus Podosphaera section Sphaerotheca belongs to the tribe Cystotheceae of the Erysiphaceae, which has the characteristic of producing catenate conidia with distinct fibrosin bodies. In this study, we newly determined the nucleotide sequences of the D1/D2 domains of the 28S rDNA region and the sequences of the rDNA internal transcribed spacer (ITS) region to investigate the relationships between the phylogeny of this fungal group and their host plants. The results indicated that the 28S rDNA region is too conservative for phylogenetic analysis of this fungal group. The phylogenetic analysis using 95 ITS sequences demonstrated that two or more Magnicellulatae taxa often infect the same plant genus or species. Although there is a close relationship between Magnicellulatae and asteraceous hosts, this association seems to be not as strict as that between Golovinomyces and the Asteraceae. The difference between the two fungal groups may be explained by their different evolutionary timing.     

Molecular phylogenetics of the hummingbird genus Coeligena

Advances in the understanding of biological radiations along tropical mountains depend on the knowledge of phylogenetic relationships among species. Here we present a species-level molecular phylogeny based on a multilocus dataset for the Andean hummingbird genus Coeligena. We compare this phylogeny to previous hypotheses of evolutionary relationships and use it as a framework to understand patterns in the evolution of sexual dichromatism and in the biogeography of speciation within the Andes. Previous phylogenetic hypotheses based mostly on similarities in coloration conflicted with our molecular phylogeny, emphasizing the unreliability of color characters for phylogenetic inference. Two major clades, one monochromatic and the other dichromatic, were found in Coeligena. Closely related species were either allopatric or parapatric on opposite mountain slopes. No sister lineages replaced each other along an elevational gradient. Our results indicate the importance of geographic isolation for speciation in this group and the potential interaction between isolation and sexual selection to promote diversification.     

Phylogeny of Salmonine Fishes Based on Growth Hormone Introns: Atlantic (Salmo) and Pacific (Oncorhynchus) Salmon Are Not Sister Taxa

Though salmonid fishes are a well-studied group, phylogenetic questions remain, especially with respect to genus-level relationships. These questions were addressed with duplicate growth hormone (GH) introns. Intron sequences from each duplicate gene yielded phylogenetic trees that were not significantly different from each other in topology. Statistical tests supported validity of the controversial monotypic genusParahucho,monophyly ofOncorhynchus,and inclusion ofAcantholingua ohridanawithinSalmo.Suprisingly, GH1 intron C (GH1C) did not support the widely accepted hypothesis thatOncorhynchus(Pacific salmon and trout) andSalmo(Atlantic salmon and trout) are sibling genera; GH2C was ambiguous at this node. Previously published data were also examined for support ofSalmoandOncorhynchusas sister taxa and only morphology showed significant support. If not sister taxa, the independent evolution of anadromy—the migration to sea and return to freshwater for spawning—is most parsimonious. While there was incongruence with and among published data sets, the GH1C intron phylogeny was the best hypothesis, based on currently available molecular data.     

Basal relationships in the Drosophila melanogaster species group

The Drosophila melanogaster species group is a popular model for evolutionary studies due to its morphological and ecological diversity and its inclusion of the model species D. melanogaster. However, phylogenetic relationships among major lineages within this species group remain controversial. In this report, the phylogeny of 10 species representing each of the well-supported monophyletic clades in the melanogaster group was studied using the sequences of 14 loci that together comprise 9493 nucleotide positions. Combined Bayesian analysis using gene-specific substitution models produced a 100% credible set of two trees. In the strict consensus of these trees, the ananassae subgroup branches first in the melanogaster species group, followed by the montium subgroup. The remaining lineages form a monophyletic clade in which D. ficusphila and D. elegans branch first, followed by D. biarmipes, D. eugracilis, and the melanogaster subgroup. This strongly supported phylogeny resolves most basal relationships in the melanogaster species group, and provides a framework that can be extended in the future to encompass more species.     

Multilocus phylogeny and systematics of Iberian endemic Squalius (Actinopterygii,Leuciscidae)

Inferring the evolutionary history of a group of species can be challenging given the many factors involved. In recent years, the increased availability of sequences of multiple genes per species has spurred the development of new methodologies to analyse multilocus data sets. Two approaches that analyse such data are concatenated supermatrix and coalescent-based species-tree analyses. In this study, we used both of these methods to infer the phylogenetic relationships of Iberian species of the genus Squalius from one mitochondrial and six nuclear genes. We found mitonuclear discordance in the phylogenetic relationships of the group. According to the mitochondrial gene analysis, all species were recovered as monophyletic except S. pyrenaicus; besides, in the concatenated supermatrix analysis of the nuclear markers, this species resolved as polyphyletic with three divergent evolutionary lineages. The coalescent-based nuclear species-tree analysis rendered a well-resolved phylogeny compared with the supermatrix analysis, which was unable to discern between S. carolitertii, S. castellanus and one of the evolutionary lineages of S. pyrenaicus. This result is likely due to the better integration of population uncertainty in the coalescent approach. Furthermore, Bayesian multilocus species delimitation analyses based on a BPP approach strongly supported the distinct nuclear lineages as different species. Nevertheless, the supermatrix analysis was able to obtain well-supported relationships in the divergent lineages with low numbers of individuals. Our study highlights the usefulness of different analytical methodologies to obtain a more complete picture of the evolutionary history of taxa, especially when discordant patterns among genes are found.     

Phylogenetic relationships and genetic diversity among members of theFestuca-Lolium complex (Poaceae) based on ITS sequence data

There have been few DNA sequencebased studies of phylogenetic relationships within theFestuca-Lolium complex. Here we infer the phylogeny of 31Festuca-Lolium taxa with a dataset of 116 ITS sequences. The results are consistent with previous studies that resolved two majorFestuca clades: one clade of fine fescues and another clade that containsLolium and associatedFestuca species. This study is unique in suggesting a third, basalFestuca clade, but support for the basal position of this group is low. Extensive sampling permitted investigation of the effects of lineage sorting and reticulate events on the evolution of the complex. Roughly half of the taxa show evidence of lineage sorting or reticulation, and the monophyly ofLolium has likely been obscured by reticulate events. Overall, polyploid species harbor higher levels of ITS sequence diversity than diploids; ITS sequence variants may provide clues to the identity of allopolyploid parents.