Evolutionary Relationships in Peromyscus: Congruence in Chromosomal, Genic, and Classical Data Sets

1984 ◽  
Vol 65 (4) ◽  
pp. 643-654 ◽  
Author(s):  
F. B. Stangl ◽  
R. J. Baker
Keyword(s):  
Evolutionary Relationships ◽  
Data Sets

Perspectives on the Evolution and Diversification of the Diatoms

2007 ◽  
Vol 13 ◽  
pp. 1-12 ◽  
Author(s):  
Matthew L. Julius
Keyword(s):  
Molecular Clock ◽  
Fossil Record ◽  
Early Jurassic ◽  
Late Triassic ◽  
Evolutionary Relationships ◽  
Data Sets ◽  
Diatom Species ◽  
Generic Level ◽  
Existing Data

The understanding of diatom evolution has progressed greatly over the last two decades. Existing data sets have been reanalyzed, new data sets have been generated, and new tools have been employed. Hindering progress is the seemingly endless number of diatom species remaining to be described and relative small number of investigators active in the field. This problem is further confounded by the dramatic reorganization of generic level classification in the group. Despite these problems, many conclusions can be made about prior hypotheses concerning the group's development. Most notably, the origin of the diatoms can be bracketed between the Late Triassic and Early Jurassic using fossil record and molecular clock estimates. This combination of techniques has also provided consensus and clarification to the origin and duration of specific lineages enhancing our understanding of the group's diversification, early ecology, and evolutionary relationships.

Bayesian Tip-Dated Phylogenetics in Paleontology: Topological Effects and Stratigraphic Fit

2020 ◽  
Author(s):  
Benedict King
Keyword(s):  
Phylogenetic Analysis ◽  
Bayesian Methods ◽  
Diversification Rate ◽  
Evolutionary Relationships ◽  
Data Sets ◽  
Tree Model ◽  
Phylogenetic Methods ◽  
History Of ◽  
Tree Topologies ◽  
Birth Death

Abstract The incorporation of stratigraphic data into phylogenetic analysis has a long history of debate but is not currently standard practice for paleontologists. Bayesian tip-dated (or morphological clock) phylogenetic methods have returned these arguments to the spotlight, but how tip dating affects the recovery of evolutionary relationships has yet to be fully explored. Here I show, through analysis of several data sets with multiple phylogenetic methods, that topologies produced by tip dating are outliers as compared to topologies produced by parsimony and undated Bayesian methods, which retrieve broadly similar trees. Unsurprisingly, trees recovered by tip dating have better fit to stratigraphy than trees recovered by other methods under both the Gap Excess Ratio (GER) and the Stratigraphic Completeness Index (SCI). This is because trees with better stratigraphic fit are assigned a higher likelihood by the fossilized birth-death tree model. However, the degree to which the tree model favors tree topologies with high stratigraphic fit metrics is modulated by the diversification dynamics of the group under investigation. In particular, when net diversification rate is low, the tree model favors trees with a higher GER compared to when net diversification rate is high. Differences in stratigraphic fit and tree topology between tip dating and other methods are concentrated in parts of the tree with weaker character signal, as shown by successive deletion of the most incomplete taxa from two data sets. These results show that tip dating incorporates stratigraphic data in an intuitive way, with good stratigraphic fit an expectation that can be overturned by strong evidence from character data. [fossilized birth-death; fossils; missing data; morphological clock; morphology; parsimony; phylogenetics.]

Evolutionary Relationships of the Australasian Mud-Nesters (Grallinidae, Corcoracidae) - Immunological Evidence

1992 ◽  
Vol 40 (2) ◽  
pp. 173 ◽  
Author(s):  
PR Baverstock ◽  
R Schodde ◽  
L Christidis ◽  
M Krieg ◽  
J Birrell
Keyword(s):  
Phylogenetic Relationships ◽  
Evolutionary Relationships ◽  
Data Sets ◽  
Dna Hybridisation ◽  
Microcomplement Fixation

The phylogenetic relationships of the genera of Australasian mud-nesters (Corcorax, Struthidea and Grallina) were examined by microcomplement fixation, and the results compared with morphological and DNA-DNA hybridisation data. There was general corroboration among all data sets such that (1) Corcorax and Struthidea were well-diverged members of a single lineage related to corvoids, and (2) Grallina comprised two species (Australian G. cyanoleuca and New Guinean G. bruijni) closely allied to Myiagra among the monarch flycatchers (Monarchidae). The immunological data also indicated that Corcorax and Struthidea were closer to Corvus (Corvinae) than to some other members of that subfamily identified by DNA-DNA hybridisation. There was further corroboration of evidence from DNA-DNA hybridisation for an endemic radiation among Australo-Papuan passerine families.

scholarly journals Unraveling Evolutionary Relationships Among the Divergent Lineages of Colletotrichum Causing Anthracnose Disease in Turfgrass and Corn

2006 ◽  
Vol 96 (1) ◽  
pp. 46-60 ◽  
Author(s):  
Jo Anne Crouch ◽  
Bruce B. Clarke ◽  
Bradley I. Hillman
Keyword(s):  
Current Data ◽  
Red Rot ◽  
Evolutionary Relationships ◽  
Data Sets ◽  
C4 Grasses ◽  
Big Bluestem ◽  
Anthracnose Disease ◽  
Colletotrichum Species ◽  
Grass Hosts

Colletotrichum species cause anthracnose diseases on a number of grass hosts and are common inhabitants of many others. They are divided into four species: C. sublineolum is pathogenic to Sorghum spp.; C. caudatum is found on C4 grasses such as indiangrass and big bluestem; C. falcatum causes red rot of sugarcane; and C. graminicola sensu lato is a broadly defined species including isolates that attack maize, wheat, oats, and many forage, turf, and amenity grasses of the subfamily Pooideae. In this paper, a combination of hierarchal- and nonhierarchal-based analyses were employed to examine evolutionary relationships among the grass-infecting Colletotrichum species, with special emphasis on isolates from turf and other grasses in the subfamily Pooideae. Reconstructions performed with data sets from over 100 Colletotrichum isolates at three variable loci using phylogenetic and network-based methodologies unambiguously supported the taxonomic separation of maize-infecting isolates of C. graminicola from the pooid-infecting strains of Colletotrichum. To reflect the evolutionary relationships that exist between these distinct lineages, we propose the resurrection of the species name C. cereale to describe the pooid-infecting isolates. There was also support for further subdivision of C. cereale, but the current data are insufficient to confidently subdivide the species, as there was some evidence of recombination between lineages of this species.

scholarly journals Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales

2017 ◽  
Author(s):  
Joseph F. Walker ◽  
Ya Yang ◽  
Michael J. Moore ◽  
Jessica Mikenas ◽  
Alfonso Timoneda ◽  
...  
Keyword(s):  
Gene Tree ◽  
West African ◽  
Evolutionary Relationships ◽  
Taxon Sampling ◽  
Data Sets ◽  
List Type ◽  
Data Set ◽  
Present Evidence ◽  
Gene Tree Discordance ◽  
Phylogenomic Analyses

ABSTRACTThe carnivorous members of the large, hyperdiverse Caryophyllales (e.g. Venus flytrap, sundews and Nepenthes pitcher plants) represent perhaps the oldest and most diverse lineage of carnivorous plants. However, despite numerous studies seeking to elucidate their evolutionary relationships, the early-diverging relationships remain unresolved.To explore the utility of phylogenomic data sets for resolving relationships among the carnivorous Caryophyllales, we sequenced ten transcriptomes, including all the carnivorous genera except those in the rare West African liana family (Dioncophyllaceae). We used a variety of methods to infer the species tree, examine gene tree conflict and infer paleopolyploidy events.Phylogenomic analyses support the monophyly of the carnivorous Caryophyllales, with an origin of 68-83 mya. In contrast to previous analyses recover the remaining non-core Caryophyllales as non-monophyletic, although there are multiple reasons this result may be spurious and node supporting this relationship contains a significant amount gene tree discordance. We present evidence that the clade contains at least seven independent paleopolyploidy events, previously debated nodes from the literature have high levels of gene tree conflict, and taxon sampling influences topology even in a phylogenomic data set.Our data demonstrate the importance of carefully considering gene tree conflict and taxon sampling in phylogenomic analyses. Moreover, they provide a remarkable example of the propensity for paleopolyploidy in angiosperms, with at least seven such events in a clade of less than 2500 species.

Evolutionary relationships among Eimeria spp. (Apicomplexa) infecting cricetid rodents

1987 ◽  
Vol 65 (3) ◽  
pp. 722-735 ◽  
Author(s):  
David W. Reduker ◽  
Donald W. Duszynski ◽  
Terry L. Yates
Keyword(s):  
Cladistic Analysis ◽  
Type A ◽  
Evolutionary Relationships ◽  
Data Sets ◽  
Type B ◽  
Generic Level ◽  
Thin Walls ◽  
Eimeria Spp ◽  
Eimeria Nieschulzi ◽  
Peromyscus Eremicus

Evolutionary relationships among seven species of Eimeria from five species of cricetid rodents (Neotoma albigula, Peromyscus eremicus, Peromyscus leucopus, Peromyscus maniculatus, Peromyscus truei) were examined by phenetic and cladistic analysis of oocyst structure, life-history data, and isozyme banding patterns. Phenetic and cladistic analyses revealed two distinct lineages of Eimeria spp.: type A Eimeria spp. (Eimeria albigulae, Eimeria arizonensis, Eimeria peromysci), characterized by subspheroid oocysts with rough outer walls, lemon-shaped sporocysts, oocyst residua, prominent Stieda bodies, and two obvious wall layers; and type B Eimeria spp. (Eimeria delicata, Eimeria lachrymalis, Eimeria ladronensis, Eimeria lange-barteli), characterized by ellipsoid oocysts with one obvious, smooth wall, no residuum, and ellipsoid or teardrop-shaped sporocysts with thin walls and tiny Stieda bodies. Cladistic analysis of the type A and type B data sets, using Eimeria nieschulzi and Eimeria papillata (hosts: Rattus norvegicus and Mus musculus, respectively) for outgroup comparison, showed the more derived nature of Eimeria spp. infecting Peromyscus spp. relative to those species infecting N. albigula. Comparison of parasite phylogenies to a hypothesized phylogeny for the hosts based on enzyme electrophoretic data revealed patterns of host–parasite phylogenetic congruence that were most evident at the generic level of the hosts.

An example of spectrum imaging used for comparison of EELS quantitative analysis techniques on Al-Li

1991 ◽  
Vol 49 ◽  
pp. 726-727
Author(s):  
John A. Hunt
Keyword(s):  
Quantitative Analysis ◽  
Large Data ◽  
Difference Spectrum ◽  
Large Data Sets ◽  
Foil Thickness ◽  
Data Sets ◽  
Analysis Techniques ◽  
Spectrum Imaging ◽  
Normal Spectrum ◽  
Electron Energy Loss

Spectrum-imaging is a useful technique for comparing different processing methods on very large data sets which are identical for each method. This paper is concerned with comparing methods of electron energy-loss spectroscopy (EELS) quantitative analysis on the Al-Li system. The spectrum-image analyzed here was obtained from an Al-10at%Li foil aged to produce δ' precipitates that can span the foil thickness. Two 1024 channel EELS spectra offset in energy by 1 eV were recorded and stored at each pixel in the 80x80 spectrum-image (25 Mbytes). An energy range of 39-89eV (20 channels/eV) are represented. During processing the spectra are either subtracted to create an artifact corrected difference spectrum, or the energy offset is numerically removed and the spectra are added to create a normal spectrum. The spectrum-images are processed into 2D floating-point images using methods and software described in [1].

Computer-aided methods for 3-D visualization of serial sections and thick biological specimens

1992 ◽  
Vol 50 (2) ◽  
pp. 1060-1061
Author(s):  
Mark Ellisman ◽  
Maryann Martone ◽  
Gabriel Soto ◽  
Eleizer Masliah ◽  
David Hessler ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Three Dimensional ◽  
Neuritic Plaque ◽  
Dimensional Structure ◽  
Data Sets ◽  
Molecular Physiology ◽  
Research Activities ◽  
Computer Aided ◽  
Dimensional Reconstruction

Structurally-oriented biologists examine cells, tissues, organelles and macromolecules in order to gain insight into cellular and molecular physiology by relating structure to function. The understanding of these structures can be greatly enhanced by the use of techniques for the visualization and quantitative analysis of three-dimensional structure. Three projects from current research activities will be presented in order to illustrate both the present capabilities of computer aided techniques as well as their limitations and future possibilities.The first project concerns the three-dimensional reconstruction of the neuritic plaques found in the brains of patients with Alzheimer's disease. We have developed a software package “Synu” for investigation of 3D data sets which has been used in conjunction with laser confocal light microscopy to study the structure of the neuritic plaque. Tissue sections of autopsy samples from patients with Alzheimer's disease were double-labeled for tau, a cytoskeletal marker for abnormal neurites, and synaptophysin, a marker of presynaptic terminals.

Direct phase determination in electron crystallography: small organic molecules

1992 ◽  
Vol 50 (2) ◽  
pp. 1166-1167
Author(s):  
Douglas L. Dorset
Keyword(s):  
Organic Molecules ◽  
Data Sets ◽  
Temperature Structure ◽  
3D Analysis ◽  
Intensity Data ◽  
Electron Crystallography ◽  
Phase Determination ◽  
Measured Intensity ◽  
3D Data

The quantitative use of electron diffraction intensity data for the determination of crystal structures represents the pioneering achievement in the electron crystallography of organic molecules, an effort largely begun by B. K. Vainshtein and his co-workers. However, despite numerous representative structure analyses yielding results consistent with X-ray determination, this entire effort was viewed with considerable mistrust by many crystallographers. This was no doubt due to the rather high crystallographic R-factors reported for some structures and, more importantly, the failure to convince many skeptics that the measured intensity data were adequate for ab initio structure determinations.We have recently demonstrated the utility of these data sets for structure analyses by direct phase determination based on the probabilistic estimate of three- and four-phase structure invariant sums. Examples include the structure of diketopiperazine using Vainshtein's 3D data, a similar 3D analysis of the room temperature structure of thiourea, and a zonal determination of the urea structure, the latter also based on data collected by the Moscow group.

Automated cell counting of astrocytes on patterned substrates containing aliphatic and charged properties

1995 ◽  
Vol 53 ◽  
pp. 974-975
Author(s):  
W. Shain ◽  
H. Ancin ◽  
H.C. Craighead ◽  
M. Isaacson ◽  
L. Kam ◽  
...  
Keyword(s):  
Cell Culture ◽  
Cell Attachment ◽  
Culture Method ◽  
Cell Counting ◽  
Data Sets ◽  
Nuclear Staining ◽  
Double Positive ◽  
A Cell ◽  
Wafer Test ◽  
Cell Densities

Neural protheses have potential to restore nervous system functions lost by trauma or disease. Nanofabrication extends this approach to implants for stimulating and recording from single or small groups of neurons in the spinal cord and brain; however, tissue compatibility is a major limitation to their practical application. We are using a cell culture method for quantitatively measuring cell attachment to surfaces designed for nanofabricated neural prostheses.Silicon wafer test surfaces composed of 50-μm bars separated by aliphatic regions were fabricated using methods similar to a procedure described by Kleinfeld et al. Test surfaces contained either a single or double positive charge/residue. Cyanine dyes (diIC18(3)) stained the background and cell membranes (Fig 1); however, identification of individual cells at higher densities was difficult (Fig 2). Nuclear staining with acriflavine allowed discrimination of individual cells and permitted automated counting of nuclei using 3-D data sets from the confocal microscope (Fig 3). For cell attachment assays, LRM5 5 astroglial cells and astrocytes in primary cell culture were plated at increasing cell densities on test substrates, incubated for 24 hr, fixed, stained, mounted on coverslips, and imaged with a 10x objective.

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