Tree Topology (tree + topology)

Distribution by Scientific Domains


Selected Abstracts


Distribution, phylogenetic diversity and physiological characteristics of epsilon- Proteobacteria in a deep-sea hydrothermal field

ENVIRONMENTAL MICROBIOLOGY, Issue 10 2005
Satoshi Nakagawa
Summary Epsilon- Proteobacteria is increasingly recognized as an ecologically significant group of bacteria, particularly in deep-sea hydrothermal environments. In this study, we studied the spatial distribution, diversity and physiological characteristics of the epsilon- Proteobacteria in various microbial habitats in the vicinity of a deep-sea hydrothermal vent occurring in the Iheya North field in the Mid-Okinawa Trough, by using culture-dependent and -independent approaches. The habitats studied were inside and outside hydrothermal plume, and annelid polychaete tubes. In addition, we deployed colonization devices near the vent emission. The polychaete tubes harboured physiologically and phylogenetically diverse microbial community. The in situ samplers were predominantly colonized by epsilon -Proteobacteria. Energy metabolism of epsilon- Proteobacteria isolates was highly versatile. Tree topology generated from the metabolic traits was significantly different (P = 0.000) from that of 16S rRNA tree, indicating current 16S rRNA gene-based analyses do not provide sufficient information to infer the physiological characteristics of epsilon- Proteobacteria. Nevertheless, culturability of epsilon- Proteobacteria in various microbial habitats differed among the phylogenetic subgroups. Members of Sulfurimonas were characterized by the robust culturability, and the other phylogenetic subgroups appeared to lose culturability in seawater, probably because of the sensitivity to oxygen. These results provide new insight into the ecophysiological characteristics of the deep-sea hydrothermal vent epsilon- Proteobacteria, which has never been assessed by comparative analysis of the 16S rRNA genes. [source]


Reverse dissimilatory sulfite reductase as phylogenetic marker for a subgroup of sulfur-oxidizing prokaryotes

ENVIRONMENTAL MICROBIOLOGY, Issue 2 2009
Alexander Loy
Summary Sulfur-oxidizing prokaryotes (SOP) catalyse a central step in the global S-cycle and are of major functional importance for a variety of natural and engineered systems, but our knowledge on their actual diversity and environmental distribution patterns is still rather limited. In this study we developed a specific PCR assay for the detection of dsrAB that encode the reversely operating sirohaem dissimilatory sulfite reductase (rDSR) and are present in many but not all published genomes of SOP. The PCR assay was used to screen 42 strains of SOP (most without published genome sequence) representing the recognized diversity of this guild. For 13 of these strains dsrAB was detected and the respective PCR product was sequenced. Interestingly, most dsrAB -encoding SOP are capable of forming sulfur storage compounds. Phylogenetic analysis demonstrated largely congruent rDSR and 16S rRNA consensus tree topologies, indicating that lateral transfer events did not play an important role in the evolutionary history of known rDSR. Thus, this enzyme represents a suitable phylogenetic marker for diversity analyses of sulfur storage compound-exploiting SOP in the environment. The potential of this new functional gene approach was demonstrated by comparative sequence analyses of all dsrAB present in published metagenomes and by applying it for a SOP census in selected marine worms and an alkaline lake sediment. [source]


Molecular phylogeny of Turkish Trachurus species (Perciformes: Carangidae) inferred from mitochondrial DNA analyses

JOURNAL OF FISH BIOLOGY, Issue 5 2008
Y. Bektas
Genetic variation among three species of Trachurus (T. trachurus, T. mediterraneus and T. picturatus) from Turkey was investigated by phylogenetic analysis of the entire mtDNA control region (CR) (862 bp, n = 182) and partial cytochrome (cyt) b (239 bp, n = 174) sequences. Individuals were collected at nine stations in four geographic locations: North-eastern Mediterranean Sea, Aegean Sea, Sea of Marmara and Black Sea. Polymerase chain reaction-direct sequencing of the CR and the partial cyt b genes produced 28 and 131 distinct haplotypes, respectively. Maximum likelihood, neighbour-joining and maximum parsimony methods produced similar tree topologies. The results of both CR and cyt b sequence analyses revealed the existence of several species-specific nucleotide sites that can be used to discriminate between the three species. Genetic distances indicated that T. mediterraneus and T. picturatus are more closely related to each other than either is to T. trachurus. Inter-nucleotide and intra-nucleotide diversities of T. picturatus were larger than those of T. mediterraneus and T. trachurus. There was no evidence of a geographical difference in haplotype frequencies of these two mtDNA regions to be clustered. [source]


BIOGEOGRAPHY OF MARINE RED ALGAE: MYTHS AND REALITIES

JOURNAL OF PHYCOLOGY, Issue 2001
Article first published online: 24 SEP 200
Hommersand, M. H. Department of Biology, Coker Hall, University of North Carolina, Chapel Hill, NC 27599-3280 USA Theories about the geographical distribution of marine algae fall roughly into two categories: (1) a concept of biogeographical regions in which algal distribution is determined primarily by growth, reproductive and lethal temperature boundaries (Setchell, van den Hoek, Breeman, Lüning) and (2) an historical perspective in which distribution is determined primarily by patterns of dispersal and the establishment of barriers to dispersal (vicariance biogeography) (Svedelius, Garbary, Lindstrom, Hommersand). Setchell proposed the 5° isotherm rule in 1920, and in 1924 Svedelius advocated a worldwide distribution for tropical and subtropical groups followed by discontinuous distribution upon closure of the connection between the Indian Ocean and Mediterranean Sea and, later, between North and South America (Wegener's theory). Transarctic dispersal routes have received special attention in recent years (Lindstrom, Lüning, van Oppen, Olsen, Stam), as have special relationships between Australasia, South Africa and South America (Hommersand). Less well understood are the climatic changes that have taken place in the Cenozoic which are strategic to an understanding vicariant biogeography. The advent of molecular methods combined with the tools of phylogenetic systematics now make it possible to identify ancestral taxa, test the consistency of tree topologies, and calculate mean branch lengths between sister lineages diverging from an interior node of a tree. With such methods it may be possible to infer ancestral areas, identify dispersal pathways, determine the chronology of isolating events, assess the impact of multiple invasions, and generally relate dispersal and vicariance models to phylogenetic hypotheses for red, brown and green algal taxa. [source]


Taxon combinations, parsimony analysis (PAUP*), and the taxonomy of the yellow-tailed woolly monkey, Lagothrix flavicauda

AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 3 2008
Luke J. Matthews
Abstract The classifications of primates, in general, and platyrrhine primates, in particular, have been greatly revised subsequent to the rationale for taxonomic decisions shifting from one rooted in the biological species concept to one rooted solely in phylogenetic affiliations. Given the phylogenetic justification provided for revised taxonomies, the scientific validity of taxonomic distinctions can be rightly judged by the robusticity of the phylogenetic results supporting them. In this study, we empirically investigated taxonomic-sampling effects on a cladogram previously inferred from craniodental data for the woolly monkeys (Lagothrix). We conducted the study primarily through much greater sampling of species-level taxa (OTUs) after improving some character codings and under a variety of outgroup choices. The results indicate that alternative selections of species subsets from within genera produce various tree topologies. These results stand even after adjusting the character set and considering the potential role of interobserver disagreement. We conclude that specific taxon combinations, in this case, generic or species pairings, of the primary study group has a biasing effect in parsimony analysis, and that the cladistic rationale for resurrecting the Oreonax generic distinction for the yellow-tailed woolly monkey (Lagothrix flavicauda) is based on an artifact of idiosyncratic sampling within the study group below the genus level. Some recommendations to minimize the problem, which is prevalent in all cladistic analyses, are proposed. Am J Phys Anthropol, 2008. © 2008 Wiley-Liss, Inc. [source]


Molecular data reveals California as the potential source of an invasive leafhopper species, Macrosteles sp. nr. severini, transmitting the aster yellows phytoplasma in Hawaii

ANNALS OF APPLIED BIOLOGY, Issue 3 2009
J.J. Le Roux
Abstract A species of aster leafhopper (Macrosteles sp.) became established in 2001 on Oahu, Hawaii, and through the transmission of the aster yellows phytoplasma, caused devastating losses to the island's watercress industry. DNA sequence data were analysed from two mitochondrial genes [cytochrome oxidase subunit 1(CO1) and nicotinamide adenine dinucleotide 1 (NADH1)] and one nuclear gene (wingless, Wg) (combined total of 1874 bp) to reconstruct phylogenetic relationships between putative US mainland source populations of aster leafhoppers and those introduced to Hawaii. These data were applied to elucidate the origin(s) and identity of Hawaiian infestations and the amount of genetic diversity within introduced invasive populations. Both phylogenetic search criteria (Bayesian and maximum likelihood models) converged onto similar tree topologies for all three gene regions and suggested that Hawaii infestations represent a single undescribed leafhopper species unrelated to the common aster leafhopper, Macrosteles quadrilineatus. An exact haplotype match was found from a specimen intercepted from watercress shipped to Hawaii from Los Angeles, California, suggesting this region as the potential source for Hawaiian infestations. Two mitochondrial haplotypes were identified in Hawaii suggesting two or perhaps just a single introduction of more than one female. [source]


Phylogeny of ,-proteobacteria: resolution of one branch of the universal tree?

BIOESSAYS, Issue 5 2004
James R. Brown
The reconstruction of bacterial evolutionary relationships has proven to be a daunting task because variable mutation rates and horizontal gene transfer (HGT) among species can cause grave incongruities between phylogenetic trees based on single genes. Recently, a highly robust phylogenetic tree was constructed for 13 ,-proteobacteria using the combined alignments of 205 conserved orthologous proteins.1 Only two proteins had incongruent tree topologies, which were attributed to HGT between Pseudomonas species and Vibrio cholerae or enterics. While the evolutionary relationships among these species appears to be resolved, further analysis suggests that HGT events with other bacterial partners likely occurred; this alters the implicit assumption of ,-proteobacteria monophyly. Thus, any thorough reconstruction of bacterial evolution must not only choose a suitable set of molecular markers but also strive to reduce potential bias in the selection of species. BioEssays 26:463,468, 2004. © 2004 Wiley Periodicals, Inc. [source]


Does the skull carry a phylogenetic signal?

BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2008
Evolution, modularity in the guenons
Form and genes often tell different stories about the evolution of animals, with molecular data generally considered to be more objective than morphological data. However, form provides the basis for the description of organisms, and the study of fossils crucially depends on morphology. Complex organisms tend to evolve as ,mosaics', in which parts may be modified at varying rates and in response to different selective pressures. Thus, individual anatomical regions may contain different phylogenetic signals. In the present study, we used computerized methods to ,dissect' the skulls of a primate clade, the guenons, into functional and developmental modules (FDM). The potential of different modules as proxies for phylogenetic divergence in modern lineages was investigated. We found that the chondrocranium was the only FDM in which shape consistently had a strong and significant phylogenetic signal. This region might be less susceptible to epigenetic factors and thus more informative about phylogeny. The examination of the topology of trees from the chondrocranium suggested that the main differences evolved at the time of the radiation of terrestrial and arboreal guenons. However, phylogenetic reconstructions were found to be strongly affected by sampling error, with more localized anatomical regions (i.e. smaller/less complex FDMs) generally producing less reproducible tree topologies. This finding, if confirmed in other groups, implies that the utility of specific FDMs for phylogenetic inference could, in many cases, be hampered by the low reproducibility of results. The study also suggested that uncertainties due to sampling error may be larger than those from character sampling. This might have implications for phylogenetic analyses, which typically provide estimates of support of tree nodes based on characters but do not generally take into account the effect of sampling error on the tree topology. Nonetheless, studies of the potential of different FDMs as proxies for phylogenetic divergence in modern lineages, such as the present study, provide a framework that may help in modelling the morphological evolution of present and fossil species. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 93, 813,834. [source]


The nematode,arthropod clade revisited: phylogenomic analyses from ribosomal protein genes misled by shared evolutionary biases

CLADISTICS, Issue 2 2007
Stuart J. Longhorn
Phylogenetic analysis of major groups of Metazoa using genomic data tends to recover the sister relationships of arthropods and chordates, contradicting the proposed Ecdysozoa (the molting animals), which group the arthropods together with nematodes and relatives. Ribosomal protein genes have been a major data source in phylogenomic studies because they are readily detected as Expressed Sequence Tags (ESTs) due to their high transcription rates. Here we address the debate about the recovery of Ecdysozoa in genomic data by building a new matrix of carefully curated EST and genome sequences for 25 ribosomal protein genes of the small subunit, with focus on new insect sequences in addition to the Diptera sequences generally used to represent the arthropods. Individually, each ribosomal protein gene showed low phylogenetic signal, but in simultaneous analysis strong support emerged for many expected groups, with support increasing linearly with increased gene number. In agreement with most studies of metazoan relationships from genomic data, our analyses contradicted the Ecdysozoa (the putative sister relationship of arthropods and nematodes), and instead supported the affinity of arthropods with chordates. In addition, relationships among holometabolan insects resulted in an unlikely basal position for Diptera. To test for biases in the data that might produce an erroneous arthropod,chordate affinity we simulated sequence data on tree topologies with the alternative arthropod,nematode sister relationships, applying a model of amino acid sequence evolution estimated from the real data. Tree searches on these simulated data still revealed an arthropod,chordate grouping, i.e., the topologies used to simulate the data were not recovered correctly. This suggests that the arthropod,chordate relationships may be obtained erroneously also from the real data even if the alternative topology (Ecdysozoa) represents the true phylogeny. Whereas denser taxon sampling in the future may recover the Ecdysozoa, our analyses demonstrate that recent phylogenomic studies may be affected by as yet unspecified biases in amino acid sequence composition in the model organisms with available genomic data. © The Willi Hennig Society 2007. [source]


Taxon sampling and seed plant phylogeny

CLADISTICS, Issue 5 2002
Catarina Rydin
We investigated the effects of taxon sampling on phylogenetic inference by exchanging terminals in two sizes of rbcL matrices for seed plants, applying parsimony and bayesian analyses to ten 38-taxon matrices and ten 80-taxon matrices. In comparing tree topologies we concentrated on the position of the Gnetales, an important group whose placement has long been disputed. With either method, trees obtained from different taxon samples could be mutually contradictory and even disagree on groups that seemed strongly supported. Adding terminals improved the consistency of results for unweighted parsimony, but not for parsimony with third positions excluded and not for bayesian analysis, particularly when the general time-reversible model was employed. This suggests that attempting to resolve deep relationships using only a few taxa can lead to spurious conclusions, groupings unlikely to be repeatable with different taxon samplings or larger data sets. The effect of taxon sampling has not generally been recognized, and phylogenetic studies of seed plants have often been based on few taxa. Such insufficient sampling may help explain the variety of phylogenetic hypotheses for seed plants proposed in recent years. We recommend that restricted data sets such as single-gene subsets of multigene studies should be reanalyzed with alternative selections of terminals to assess topological consistency. [source]


Is the originality of a species measurable?

ECOLOGY LETTERS, Issue 6 2005
Sandrine Pavoine
Abstract In this paper, we introduce the concept of ,originality of a species within a set' in order to indicate the average rarity of all the features belonging to this species. Using a phylogenetic tree of 70 species of New World terrestrial Carnivora, we suggest measuring the originality by a probability distribution. This maximizes the expected number of features shared by two species randomly drawn from the set. By using this new index, we take account of branch lengths whereas current indices of originality focus on tree topology. As a supplement to Nee and May's optimizing algorithm, we find that originality must be one of the criteria used in conservation planning. [source]


Directional asymmetry of long-distance dispersal and colonization could mislead reconstructions of biogeography

JOURNAL OF BIOGEOGRAPHY, Issue 5 2005
Lyn G. Cook
Abstract Aim, Phylogenies are increasingly being used to attempt to answer biogeographical questions. However, a reliance on tree topology alone has emerged without consideration of earth processes or the biology of the organisms in question. Most ancestral-state optimization methods have inherent problems, including failure to take account of asymmetry, such as unequal probabilities of losses and gains, and the lack of use of independent cost estimates. Here we discuss what we perceive as shortcomings in most current tree-based biogeography interpretation methods and show that consideration of processes and their likelihoods can turn the conventional biogeographical interpretation on its head. Location, Southern hemisphere focus but applicable world-wide. Methods, The logic of existing methods is reviewed with respect to their adequacy in modelling processes such as geographical mode of speciation and likelihood of dispersal, including directional bias. Published reconstructions of dispersal of three plant taxa between Australia and New Zealand were re-analysed using standard parsimony and maximum likelihood (ML) methods with rate matrices to model expected asymmetry of dispersal. Results, Few studies to date incorporate asymmetric dispersal rate matrices or question the simplistic assumption of equal costs. Even when they do, cost matrices typically are not derived independently of tree topology. Asymmetrical dispersal between Australia and New Zealand could be reconstructed using parsimony but not with ML. Main conclusions, The inadequacy of current models has important consequences for our interpretation of southern hemisphere biogeography, particularly in relation to dispersal. For example, if repeated directional dispersals and colonization in the direction of prevailing winds have occurred, with intervening periods of speciation, then there is no need to infer dispersals against those winds. Failure to take account of directionality and other biases in reconstruction methods has implications beyond the simple misinterpretation of the biogeography of a taxonomic group, such as calibration of molecular clocks, the dating of vicariance events, and the prioritization of areas for conservation. [source]


THE PHYLOGENY OF CAULERPA BASED ON RDNA INTERNAL TRANSCRIBED SPACER SEQUENCES

JOURNAL OF PHYCOLOGY, Issue 2000
S. Nemeth
Phylogenetic hypotheses for the pantropical marine green algal genus, Caulerpa, were inferred based on analyses of nuclear-encoded rDNA internal transcribed spacer (ITS) sequences. Results of these analyses were used to assess the correspondence between rDNA phylogeny and traditional sectional taxonomy, to identify synapomorphic morphological characters (including assimilator morphology and chloroplast ultrastructure), and to examine marine biogeographic hypotheses for the genus. Ribosomal DNA ITS sequences were aligned for thirty-three species and intraspecific taxa of Caulerpa. Results indicate limited correspondence between phylogeny and sectional taxonomy for the genus, (e.g., the sections Filicoideae and Sedoideae were not monophyletic). In contrast, chloroplast morphology could be mapped to the tree topology with limited homoplasy. Pantropical isolates of the filicoidean species, Caulerpa sertularioides and Caulerpa mexicana each formed monophyletic groups. Caulerpa reyesii was included as a derived taxon within the Caulerpa taxifolia clade, suggesting that these species were conspecific and affirmed the lack of correspondence between phylogeny and assimilator morphology. Isolates and various intraspecific taxa of Caulerpa racemosa did not form a monophyletic group. Instead, these taxa formed a heterogeneous assemblage with other sedoidean and filicoidean taxa. Within the C. sertularioides clade, Caribbean and Atlantic isolates formed a basal paraphyletic group, whereas eastern and western Pacific isolates formed a more derived monophyletic group. Therefore, these results are not consistent with an Indo-West Pacific origin of this species. [source]


Geographic variation in loud calls of sportive lemurs (Lepilemur ssp.) and their implications for conservation

AMERICAN JOURNAL OF PRIMATOLOGY, Issue 9 2008
Maria Méndez-Cárdenas
Abstract Bioacoustical studies in nonhuman primates have shown that loud calls can be reliably used as a noninvasive diagnostic tool for discriminating cryptic taxa, for their monitoring in the field as well as for the reconstruction of their phylogeny. To date, it is unknown, whether loud calls can be used for these purposes in sportive lemurs, for which current genetic studies suggest the existence of at least 24 cryptic species. The aim of this study was to compare the structure of loud calls of populations of sportive lemurs to characterize informative acoustic traits for taxa discrimination and to establish a phylogenetic tree based on acoustic structure. We have based our study on Inter-River-Systems (IRSs) as operational taxonomic units. Samples were collected from nine different localities of four IRSs along a transect from northwestern to northern Madagascar. Two call types, the ouah and the high-pitched call, were present in almost all IRSs. Six temporal and eight spectral parameters were measured in 196 calls of the best quality given by 21 different males. Variation within and between IRSs was assessed by multivariate statistics. Loud calls differed significantly among the different IRSs. The IRSs varied most in spectral parameters, whereas temporal parameters were less variable. Phylogenetic analysis using parsimony yielded 11 out of 17 acoustic characters as phylogenetically informative. The acoustic tree had an average branch support of 78%. Its topology coincided less with geographic distances than with genetic tree topology. Altogether our findings revealed that loud calls separated geographically isolated populations of sportive lemurs specifically. Based on these results, noninvasive tools for diagnosis and monitoring of cryptic species in nature can be developed for conservation management. Am. J. Primatol. 70:828,838, 2008. © 2008 Wiley-Liss, Inc. [source]


Does the skull carry a phylogenetic signal?

BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2008
Evolution, modularity in the guenons
Form and genes often tell different stories about the evolution of animals, with molecular data generally considered to be more objective than morphological data. However, form provides the basis for the description of organisms, and the study of fossils crucially depends on morphology. Complex organisms tend to evolve as ,mosaics', in which parts may be modified at varying rates and in response to different selective pressures. Thus, individual anatomical regions may contain different phylogenetic signals. In the present study, we used computerized methods to ,dissect' the skulls of a primate clade, the guenons, into functional and developmental modules (FDM). The potential of different modules as proxies for phylogenetic divergence in modern lineages was investigated. We found that the chondrocranium was the only FDM in which shape consistently had a strong and significant phylogenetic signal. This region might be less susceptible to epigenetic factors and thus more informative about phylogeny. The examination of the topology of trees from the chondrocranium suggested that the main differences evolved at the time of the radiation of terrestrial and arboreal guenons. However, phylogenetic reconstructions were found to be strongly affected by sampling error, with more localized anatomical regions (i.e. smaller/less complex FDMs) generally producing less reproducible tree topologies. This finding, if confirmed in other groups, implies that the utility of specific FDMs for phylogenetic inference could, in many cases, be hampered by the low reproducibility of results. The study also suggested that uncertainties due to sampling error may be larger than those from character sampling. This might have implications for phylogenetic analyses, which typically provide estimates of support of tree nodes based on characters but do not generally take into account the effect of sampling error on the tree topology. Nonetheless, studies of the potential of different FDMs as proxies for phylogenetic divergence in modern lineages, such as the present study, provide a framework that may help in modelling the morphological evolution of present and fossil species. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 93, 813,834. [source]


The genetic population structure of Buthus occitanus (Scorpiones: Buthidae) across the Strait of Gibraltar: calibrating a molecular clock using nuclear allozyme variation

BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2004
BENJAMIN GANTENBEIN
I assess here the importance of the Strait of Gibraltar as a barrier to gene flow for populations of the scorpion Buthus occitanus. This polytypic buthid scorpion occurs in Europe and in North Africa where it is morphologically more diverse. The phylogenetic relationship between B. occitanus populations across the Strait of Gibraltar is investigated by nuclear allozymes analysis (15 loci scored). Phylogenetic analysis based on estimated gene frequency data results in a tree topology that divides the populations into three clades, i.e. a European, an Atlas (= Morocco samples) and a Tell-Atlas clade (= Tunisian samples). The Tell-Atlas clade grouped with the European clade with a rather high bootstrap support of 70%. Within these clades low levels of genetic variability are observed. Calibrating a molecular clock under the assumption that the European populations are autochthonous and have been isolated from the North African for at least 5.33 Myr reveals a divergence rate of 0.060 genetic distance (D) per Myr estimated between European and Moroccan samples and 0.036D Myr,1 between European and Tunisian samples, respectively. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 81, 519,534. [source]


Molecular systematics of cowries (Gastropoda: Cypraeidae) and diversification patterns in the tropics

BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 3 2003
CHRISTOPHER P. MEYER
This study produces a nearly comprehensive phylogeny for the marine gastropod group Cypraeidae (cowries) and uses this topology to examine diversification patterns in the tropics. The dataset is based on molecular sequence data from two mitochondrial genes and includes 210 evolutionary significant units (ESUs) from 170 recognized species (>80%). Systematics for the group is revised based on well-supported clades, and tree topology is generally consistent with previously proposed classification schemes. Three new genera are introduced (Cryptocypraea gen. nov, Palmulacypraea gen. nov, and Contradusta gen. nov) and two previous genera are resurrected (Perisserosa and Eclogavena). One new tribe is proposed (Bistolidini). Topologies produced by a range of transition:transversion (Ti:Tv) weighting schemes in parsimony are pooled and evaluated using maximum likelihood criteria. Extensive geographical coverage shows persistent, large-scale geographical structure in sister-groups. Genetic divergence between subspecies is often equivalent or even greater than that between recognized species. Using ESUs as a metric, diversity throughout the Indo-West Pacific (IWP) increases by 38%. Intra- and inter-regional diversification patterns show that the IWP is the centre for speciation in cowries. The other major tropical regions of the world are inhabited by a predominantly relictual fauna; from a cowrie's eye-view. Good dispersal ability begets larger ranges, increased extinction resistance and morphological stasis; whereas shorter larval duration results in smaller ranges, higher speciation rates, but also higher turnover. Larval duration and dispersal ability appear correlated with ocean productivity as taxa with longer-lived larvae are associated with oligotrophic conditions; whereas taxa with shorter larval durations are associated with eutrophic, continental conditions. This tendency is carried to the extreme in temperate or upwelling regions where a planktonic phase is completely lost and crawl-away larvae evolve multiple times. A strong phylogenetic trend supports these observations as lineages leading up to and including the derived Indo-West Pacific Erroneinae clade contain taxa predominantly restricted to continental habitats and have undergone the greatest evolutionary radiations in their respective regions. © 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 79, 401, 459. [source]


Phylogeny and biogeography of Crinum L. (Amaryllidaceae) inferred from nuclear and limited plastid non-coding DNA sequences

BOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 3 2003
ALAN W. MEEROW
The genus Crinum L. is the only pantropical genus of the Amaryllidaceae. Phylogenetic and biogeographical analyses of nrDNA ITS and plastid trnL-F sequences for all continental groups of the genus Crinum and related African genera are presented, with the genus Amaryllis used as outgroup. ITS indicates that C. baumii is more closely related to Ammocharis and Cybistetes than to Crinum sensu stricto. Three clades are resolved in Crinum s.s. One unites a monophyletic American group with tropical and North African species. The second includes all southern African species and the Australian endemic C. flaccidum. The third includes monophyletic Madagascar, Australasian and Sino-Himalayan clades, with southern African species. The trnL-F phylogeny resolves an American and an Asian/Madagscar clade, and confirms the relationship of C. flaccidum with species endemic to southern Africa. The salverform, actinomorphic perianths of subg. Crinum appear to have evolved several times in the genus from ancestors with zygomorphic perianths (subg. Codonocrinum), thus neither subgenus is monophyletic. Biogeographical analyses place the origin of Crinum in southern Africa, as the region is optimized at all ancestral nodes in the tree topology, and in basal interior nodes of all but one of the major clades. The genus underwent three major waves of radiation corresponding to the three main clades resolved in our trees. Two entries into Australia for the genus are indicated, as are separate Sino-Himalayan and Australasian dispersal events. © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society, 2003, 141, 349,363. [source]


Mitochondrial genome data alone are not enough to unambiguously resolve the relationships of Entognatha, Insecta and Crustacea sensu lato (Arthropoda)

CLADISTICS, Issue 6 2004
Stephen L. Cameron
An analysis of the relationships of the major arthropod groups was undertaken using mitochondrial genome data to examine the hypotheses that Hexapoda is polyphyletic and that Collembola is more closely related to branchiopod crustaceans than insects. We sought to examine the sensitivity of this relationship to outgroup choice, data treatment, gene choice and optimality criteria used in the phylogenetic analysis of mitochondrial genome data. Additionally we sequenced the mitochondrial genome of an archaeognathan, Nesomachilis australica, to improve taxon selection in the apterygote insects, a group poorly represented in previous mitochondrial phylogenies. The sister group of the Collembola was rarely resolved in our analyses with a significant level of support. The use of different outgroups (myriapods, nematodes, or annelids + mollusks) resulted in many different placements of Collembola. The way in which the dataset was coded for analysis (DNA, DNA with the exclusion of third codon position and as amino acids) also had marked affects on tree topology. We found that nodal support was spread evenly throughout the 13 mitochondrial genes and the exclusion of genes resulted in significantly less resolution in the inferred trees. Optimality criteria had a much lesser effect on topology than the preceding factors; parsimony and Bayesian trees for a given data set and treatment were quite similar. We therefore conclude that the relationships of the extant arthropod groups as inferred by mitochondrial genomes are highly vulnerable to outgroup choice, data treatment and gene choice, and no consistent alternative hypothesis of Collembola's relationships is supported. Pending the resolution of these identified problems with the application of mitogenomic data to basal arthropod relationships, it is difficult to justify the rejection of hexapod monophyly, which is well supported on morphological grounds. © The Willi Hennig Society 2004. [source]


Systematics and Biogeography of Hard Ticks, a Total Evidence Approach

CLADISTICS, Issue 1 2000
J.S.H. Klompen
Systematic relationships among the basal Ixodidae are examined using one morphological and three molecular data sets, 18S and 28S nuclear and 16S mitochondrial rDNA. Although different combinations of partitions are incompatible in a partition homogeneity test, combining them produces similar or better support for most major lineages through both additive and complementary effects. The different data sets are not complete for all taxa, but inclusion or exclusion of taxa with missing data for one or more data sets (8 of 29 ingroup taxa) does not influence overall tree topology and only weakly affects support levels. The only notable effect was based on gap treatment in the 28S data set. Gap treatment completely changes the arrangement and support levels for one basal node. The combined analyses show strong support for the Metastriata, a lineage including most endemic Australian Ixodes, and a lineage including the remaining Ixodes, but not for the Prostriata (=Ixodes s.l.). The distribution pattern of endemic Australian taxa (nearly all included in three exclusively Australian basal lineages) suggests that these lineages, and by extension the Ixodidae, originated after the isolation of Australia in the late Cretaceous, much more recently than previously indicated. [source]