A phylogenetic investigation of Carthamus combining sequence and microsatellite data

Carthamus (Asteraceae) includes both crop (Carthamus tinctorius, safflower) and weedy species. Despite previous studies, many outstanding questions remain regarding the phylogenetic surroundings of safflower, especially in relation to weedy species. Here we investigated relationships within Carthamus using a tiered approach examining sequence and microsatellite data. First, nuclear and chloroplast sequences were analyzed from 37 accessions of 16 species. Maximum parsimony, maximum likelihood, and Bayesian inference confirm two well supported clades, corresponding to sect. Atractlyis and sect. Carthamus, the latter of which includes safflower. Because sequence data provided limited resolution within the clades, microsatellite markers were used to investigate relationships within sect. Carthamus. Both sequence and microsatellite data reveal that most traditionally recognized species are not monophyletic. Microsatellite data indicate that Carthamus palaestinus is the closest relative of cultivated safflower.     

Visualizations for taxonomic and phylogenetic trees

MOTIVATION: Despite substantial efforts to develop and populate the back-ends of biological databases, front-ends to these systems often rely on taxonomic expertise. This research applies techniques from human-computer interaction research to the biodiversity domain. RESULTS: We developed an interactive node-link tool, TaxonTree, illustrating the value of a carefully designed interaction model, animation, and integrated searching and browsing towards retrieval of biological names and other information. Users tested the tool using a new, large integrated dataset of animal names with phylogenetic-based and classification-based tree structures. These techniques also translated well for a tool, DoubleTree, to allow comparison of trees using coupled interaction. Our approaches will be useful not only for biological data but as general portal interfaces.     

Estimating diversification rates from phylogenetic information

Patterns of species richness reflect the balance between speciation and extinction over the evolutionary history of life. These processes are influenced by the size and geographical complexity of regions, conditions of the environment, and attributes of individuals and species. Diversity within clades also depends on age and thus the time available for accumulating species. Estimating rates of diversification is key to understanding how these factors have shaped patterns of species richness. Several approaches to calculating both relative and absolute rates of speciation and extinction within clades are based on phylogenetic reconstructions of evolutionary relationships. As the size and quality of phylogenies increases, these approaches will find broader application. However, phylogeny reconstruction fosters a perceptual bias of continual increase in species richness, and the analysis of primarily large clades produces a data selection bias. Recognizing these biases will encourage the development of more realistic models of diversification and the regulation of species richness.     

A phylogenetic hypothesis for passerine birds: taxonomic and biogeographic implications of an analysis of nuclear DNA sequence data

Passerine birds comprise over half of avian diversity, but have proved difficult to classify. Despite a long history of work on this group, no comprehensive hypothesis of passerine family-level relationships was available until recent analyses of DNA-DNA hybridization data. Unfortunately, given the value of such a hypothesis in comparative studies of passerine ecology and behaviour, the DNA-hybridization results have not been well tested using independent data and analytical approaches. Therefore, we analysed nucleotide sequence variation at the nuclear RAG-1 and c-mos genes from 69 passerine taxa, including representatives of most currently recognized families. In contradiction to previous DNA-hybridization studies, our analyses suggest paraphyly of suboscine passerines because the suboscine New Zealand wren Acanthisitta was found to be sister to all other passerines. Additionally, we reconstructed the parvorder Corvida as a basal paraphyletic grade within the oscine passerines. Finally, we found strong evidence that several family-level taxa are misplaced in the hybridization results, including the Alaudidae, Irenidae, and Melanocharitidae. The hypothesis of relationships we present here suggests that the oscine passerines arose on the Australian continental plate while it was isolated by oceanic barriers and that a major northern radiation of oscines (i.e. the parvorder Passerida) originated subsequent to dispersal from the south.     

Integration of morphological data sets for phylogenetic analysis of Amniota: the importance of integumentary characters and increased taxonomic sampling

Several mutually exclusive hypotheses have been advanced to explain the phylogenetic position of turtles among amniotes. Traditional morphology-based analyses place turtles among extinct anapsids (reptiles with a solid skull roof), whereas more recent studies of both morphological and molecular data support an origin of turtles from within Diapsida (reptiles with a doubly fenestrated skull roof). Evaluation of these conflicting hypotheses has been hampered by nonoverlapping taxonomic samples and the exclusion of significant taxa from published analyses. Furthermore, although data from soft tissues and anatomical systems such as the integument may be particularly relevant to this problem, they are often excluded from large-scale analyses of morphological systematics. Here, conflicting hypotheses of turtle relationships are tested by (1) combining published data into a supermatrix of morphological characters to address issues of character conflict and missing data; (2) increasing taxonomic sampling by more than doubling the number of operational taxonomic units to test internal relationships within suprageneric ingroup taxa; and (3) increasing character sampling by approximately 25% by adding new data on the osteology and histology of the integument, an anatomical system that has been historically underrepresented in morphological systematics. The morphological data set assembled here represents the largest yet compiled for Amniota. Reevaluation of character data from prior studies of amniote phylogeny favors the hypothesis that turtles indeed have diapsid affinities. Addition of new ingroup taxa alone leads to a decrease in overall phylogenetic resolution, indicating that existing characters used for amniote phylogeny are insufficient to explain the evolution of more highly nested taxa. Incorporation of new data from the soft and osseous components of the integument, however, helps resolve relationships among both basal and highly nested amniote taxa. Analysis of a data set compiled from published sources and data original to this study supports monophyly of Amniota, Synapsida, Reptilia, Parareptilia, Eureptilia, Eosuchia, Diapsida, Neodiapsida, Sauria, Lepidosauria, and Archosauriformes, as well as several more highly nested divisions within the latter two clades. Turtles are here resolved as the sister taxon to a monophyletic Lepidosauria (squamates + Sphenodon), a novel phylogenetic position that nevertheless is consistent with recent molecular and morphological studies that have hypothesized diapsid affinities for this clade.     

The microstructure of dentine in taxonomic and phylogenetic studies

Traditionally, physical anthropologists have focused their dental studies on features of teeth that can be observed with the unaided eye, measured with calipers, or observed with light microscopes. With the advent of the scanning electron microscope, there has been renewed interest in the use of the microstructure of enamel in phylogenetic reconstruction and taxonomic classification. The microstructure of dentine has received far less research attention than has enamel although several investigators have proposed that dentine has taxon specificity. We report the first results of a study in which we investigated the taxon specificity of dentine. In our study, we exposed the dentinal tubules on the mesial root surfaces of 12 Canis, 11 Papio, and 12 Homo mandibular first molars and compared tubule density and pattern among the three taxa. Based on these parameters, 91.43% of the teeth were correctly identified as being dog, baboon, or human, respectively. We conclude that dentine has taxon-specific structural characteristics, which can be used in anthropological investigations. To our knowledge, this is the first comparative study of the micro-structure of teeth utilizing statistical analysis.     

TBMap: a taxonomic perspective on the phylogenetic database TreeBASE

Background  

TreeBASE is currently the only available large-scale database of published organismal phylogenies. Its utility is hampered by a lack of taxonomic consistency, both within the database, and with names of organisms in external genomic, specimen, and taxonomic databases. The extent to which the phylogenetic knowledge in TreeBASE becomes integrated with these other sources is limited by this lack of consistency.     

Understanding angiosperm diversification using small and large phylogenetic trees

How will the emerging possibility of inferring ultra-large phylogenies influence our ability to identify shifts in diversification rate? For several large angiosperm clades (Angiospermae, Monocotyledonae, Orchidaceae, Poaceae, Eudicotyledonae, Fabaceae, and Asteraceae), we explore this issue by contrasting two approaches: (1) using small backbone trees with an inferred number of extant species assigned to each terminal clade and (2) using a mega-phylogeny of 55473 seed plant species represented in GenBank. The mega-phylogeny approach assumes that the sample of species in GenBank is at least roughly proportional to the actual species diversity of different lineages, as appears to be the case for many major angiosperm lineages. Using both approaches, we found that diversification rate shifts are not directly associated with the major named clades examined here, with the sole exception of Fabaceae in the GenBank mega-phylogeny. These agreements are encouraging and may support a generality about angiosperm evolution: major shifts in diversification may not be directly associated with major named clades, but rather with clades that are nested not far within these groups. An alternative explanation is that there have been increased extinction rates in early-diverging lineages within these clades. Based on our mega-phylogeny, the shifts in diversification appear to be distributed quite evenly throughout the angiosperms. Mega-phylogenetic studies of diversification hold great promise for revealing new patterns, but we will need to focus more attention on properly specifying null expectation.     

25S ribosomal RNA homologies of basidiomycetous yeasts: taxonomic and phylogenetic implications

Genera, families, and possibly orders of basidiomycetous yeasts can be defined by 25S rRNA homology and correlated phenotypic characters. The teleomorphic genera Filobasidium, Leucosporidium, and Rhodosporidium have greater than 96 relative binding percent (rb%) intrageneric 25S rRNA homology and significant intergeneric separation from each other and from Filobasidiella. The anamorphic genus Cryptococcus can be defined by morphology (monopolar budding), colony color, and greater than 75 rb% intrageneric homology; Vanrija is heterogeneous. Agaricostilbum (Phragmobasidiomycetes, Auriculariales), Hansenula (Ascomycotera, Endomycota), Tremella (Phragmobasidiomycetes, Tremellales), and Ustilago (Ustomycota, Ustilaginales) appear equally unrelated to the Cryptococcus, Filobasidiella, and Rhodosporidium spp. used as probes. The Filobasidiaceae and Sporidiaceae, Filobasidiales and Sporidiales, form coherent homology groups which appear to have undergone convergent 25S rRNA evolution, since their relatedness is much greater than that indicated by 5S rRNA homology. Ribosomal RNA homologies do not appear to measure evolutionary distance.     

Global patterns of taxonomic and phylogenetic endemism in liverwort assemblagesOA

Exploring the worldwide patterns of endemism and the processes that lead to the formation of highendemism centers is crucial in biogeography. This study examines the geographic distribution and ecological influences on the endemism of liverworts across 390 regions worldwide. We assess phylogenetic endemism and relative phylogenetic endemism in relation to eleven environmental factors,which represent current and Quaternary climate variations, as well as topographic and environmental heterogeneity. Areas with higher endemism in liverworts tend to have higher temperatures, precipitation, and environmental heterogeneity, but lower temperature seasonality and lesser impacts from Quaternary climate changes. Regions exhibiting notably high endemism are predominantly found in tropical Asia, Madagascar, eastern Australia, and the Andes, while those with notably low endemism are generally in temperate Eurasia and North America, parts of Africa, and eastern South America. Centers of neo-endemism are mainly in southern Africa, whereas centers of paleo-endemism are in southern South America, tropical Asia, and New Zealand. Environment variability is a more significant predictor of phylogenetic endemism than current climate conditions, which are themselves more predictive than variables related to Quaternary climate changes. Nevertheless, these three types of explanatory variables combined explain only about one-third of the variance in phylogenetic endemism.     

Ecology predicts large-scale patterns of phylogenetic diversification in birds

One of the most striking patterns in evolutionary biology is that clades may differ greatly in the number of species they contain. Numerous hypotheses have been put forward to explain this phenomenon, and several have been tested using phylogenetic methods. Remarkably, however, all such tests performed to date have been characterized by modest explanatory power, which has generated an interest in explanations stressing the importance of random processes. Here we make use of phylogenetic methods to test whether ecological variables, typically ignored in previous models, may explain phylogenetic tree imbalance in birds. We show that diversification rate possesses an intermediate phylogenetic signal across families. Using phylogenetic comparative methods, we then build a multipredictor model that explains more than 50% of the variation in diversification rate among clades. High annual dispersal is identified as the strongest predictor of high rates of diversification. In addition, high diversification rate is strongly associated with feeding generalization. In all but one instance, these key findings remain qualitatively unchanged when we use an alternative phylogeny and methodology and when small clades, containing five species or less, are excluded. Taken together, these results suggest that large-scale patterns in avian diversification can be explained by variation in intrinsic biology.     

Diversity measurement combining relative abundances and taxonomic distinctiveness of species

We discuss a diversity measure combining information of relative abundances and taxonomic distinctiveness suggested by Ricotta (2004). We show that Ricotta's measure violates weak species monotonicity, a condition that requires that the addition of a species should always increase a diversity index if abundances change only marginally. We suggest an alternative index satisfying weak species monotonicity and apply it to the 'Zeesserveld' forest reserve in the Netherlands.     

The morphology of the upper lip of Cypridoidea ostracods: taxonomic and phylogenetic significance

This paper represents the first study of the morphology of the upper lip (labrum) and hypostome of ostracods using scanning electron microscopy (S.E.M.). There is considerable variation in the upper lip morphology of the 23 species of Cypridoidea (Podocopina) ostracods used in this study. The detail of the upper lip morphology of each species is very distinctive, so that species determination can be made on this feature alone, but it is not useful in diagnosing genera or subfamilies. The hypostome is not readily studied due to the large amounts of dense pseudochaetae (small, setae-like projections) protruding from it and hence is considered not to be a useful taxonomic feature. Several features of the upper lip and mouth region are documented for the first time. Comparisons of the general morphology of the upper lips of Recent ostracods with the upper lip of the fossil ostracod Pattersoncypris micropapillosa Bate, 1972, indicate that there has been very conservative evolution in these features since the Cretaceous.     

Ecological and phylogenetic approaches for diversification of apogamous ferns in Japan

It has long been argued that related asexual and sexual taxa have different distribution patterns. In general, apomictic angiosperms are believed to occur preferentially at higher latitudes and elevations compared to their sexual relatives. It is thus expected that the frequency of apomixis increases with latitude or from warmer to colder climatic regions. However, despite the significant role played by apogamy in fern evolution and diversification, the distribution pattern of apogamous ferns and lycophytes has received little attention. To clarify the ecological diversity pattern and evolutional diversification of apogamous ferns, we analysed a variety of apogamous fern species with reference to latitude, elevation and climatic factors, and reconstructed the ancestral state and estimated the divergence time of Japanese apogamous ferns. Our results on the distribution of apogamous ferns along these two gradients suggest a decline in the proportion of apogamous ferns towards high latitudes and elevations. Temperature was correlated with the proportion of apogamous ferns along both gradients, and the seasonality of precipitation was correlated with the proportion of apogamous ferns along latitude. Reconstruction of ancestral state and estimates of divergence time showed that the crown groups of apogamous ferns diversified less than 15 Ma. The results of our ecological and phylogenetic approaches reinforce the hypothesis based on previously reported phylogenetic results in which the apogamous ferns appears to be correlated with strongly seasonal climates such as the Asia monsoon.     

Spectrum: spectral analysis of phylogenetic data

MOTIVATION: Spectrum is a new Macintosh and Microsoft Windows programdesigned to read in phylogenetic four-state or binary data in NEXUS format,and output the corresponding bipartition spectra. It can be used to findthe tree whose expected spectrum is closest to the observed spectrum (theclosest tree, Hendy, Discr, Math., 96, 51-58,. 1991).     

棕颈钩嘴鹛分子系统发育及分类关系初探

棕颈钩嘴鹛(Pomatorhinus ruficollis)各亚种间系统发育关系一直存在分歧。该文测定了棕颈钩嘴鹛10个亚种20个样本的完整线粒体Cyt b和ND2基因序列(共2184bp),以棕颈钩嘴鹛(P.ruficollis)和灰头钩嘴鹛(P.schisticeps)为内群;栗背钩嘴鹛(P.montanus)、棕头钩嘴鹛(P.ochraceiceps)、红嘴钩嘴鹛(P.ferruginosus)和剑嘴鹛(Xiphirhynchus superciliaris)为外群,通过最大简约法、最大似然法以及贝叶斯推断法,构建了棕颈钩嘴鹛亚种间的系统发育树。结果显示:棕颈钩嘴鹛是并系群,灰头钩嘴鹛聚合在其内部;棕颈钩嘴鹛可分为3个地理支序,即中国西南部支序、中国东南部支序和中国中部支序;棕颈钩嘴鹛亚种间系统发育关系与形态特征不完全一致,并澄清了一些分类问题。     

A taxonomic reassessment of the Vittiaceae (Hypnales, Bryopsida): evidence from phylogenetic analyses of combined chloroplast and nuclear sequence data

The Vittiaceae are a small family of aquatic mosses that are defined based on gametophytic traits whose interpretation has led to conflicting taxonomic arrangements. Phylogenetic analyses of two cpDNA regions, trnL-trnF and atpB-rbcL, indicate that Vittia is nested within the Amblystegiaceae s. str., suggesting that the family Vittiaceae should not be recognized. Platylomella lescurii appears nested within the Thuidiaceae/Leskeaceae. This suggests that the series of character states shared by Vittia and Platylomella, including a differentiated leaf border, short laminal cells, stiff stems, and a thick costa, are convergent features that arose independently in unrelated lineages of aquatic Hypnales. Within the Amblystegiaceae, phylogenetic analyses of the two cpDNA regions combined with ITS sequence data show that Hypnobartlettia, Vittia elimbata spec. nov., V. pachyloma, and V. salina, despite their strong morphological similarity to aquatic Amblystegium species, form a clade that is sister to the Drepanocladus/Pseudo-calliergon complex. This combined clade is unresolved at a polytomy that includes Amblystegium serpens and a clade including all the other Amblystegium species. The occurrence of A. serpens outside the strongly supported clade including other Amblystegium species suggests that A. serpens may be better accommodated in a distinct genus. Amblystegium serpens is the type species of Amblystegium and thus retains the name. The other species are accommodated in their own genus, Hygroamblystegium, including H. fluviatile, H. humile comb. nov., H. noterophyllum, H. tenax, and H. varium.