scholarly journals Data Types and the Phylogeny of Neoaves

2020 ◽  
Author(s):  
Edward L. Braun ◽  
Rebecca T. Kimball
Keyword(s):  
Analytical Method ◽  
Base Composition ◽  
Phylogenetic Analyses ◽  
Data Type ◽  
Data Types ◽  
Rapid Radiation ◽  
Simple Analytical Method ◽  
Taxonomic Groups ◽  
Purines And Pyrimidines

The phylogeny of Neoaves, the largest clade of extant birds, has remained unclear despite intense study. The difficulty associated with resolving the early branches in Neoaves is likely driven by the rapid radiation of this group. However, conflicts among studies may be exacerbated by the hypothesis that relationships are sensitive to the data type analyzed. For example, analyses of coding exons typically yield trees that place Strisores (nightjars and allies) sister to the remaining Neoaves, while analyses of non-coding data typically yield trees where Mirandornites (flamingos and grebes) is the sister of the remaining Neoaves. Our understanding of data type effects is hampered by the fact that previous analyses have used different taxa, loci, and types of non-coding data. Herein, we provide strong corroboration of the data type effects hypothesis for Neoaves by comparing trees based on coding and non-coding data derived from the same taxa and gene regions. A simple analytical method known to minimize biases due to base composition (coding nucleotides as purines and pyrimidines) resulted in coding exon data with increased congruence to the non-coding topology using concatenated analyses. These results improve our understanding of the resolution of neoavian phylogeny and point to a challenge - data type effects - that is likely to be an important factor in phylogenetic analyses of birds (and many other taxonomic groups). Using our results, we provide a summary phylogeny that identifies well-corroborated relationships and highlights specific nodes where future efforts should focus.

scholarly journals Data Types and the Phylogeny of Neoaves

Birds ◽  
2021 ◽  
Vol 2 (1) ◽  
pp. 1-22
Author(s):  
Edward L. Braun ◽  
Rebecca T. Kimball
Keyword(s):  
Analytical Method ◽  
Base Composition ◽  
Phylogenetic Analyses ◽  
Data Type ◽  
Data Types ◽  
Rapid Radiation ◽  
Simple Analytical Method ◽  
Taxonomic Groups ◽  
Purines And Pyrimidines

The phylogeny of Neoaves, the largest clade of extant birds, has remained unclear despite intense study. The difficulty associated with resolving the early branches in Neoaves is likely driven by the rapid radiation of this group. However, conflicts among studies may be exacerbated by the data type analyzed. For example, analyses of coding exons typically yield trees that place Strisores (nightjars and allies) sister to the remaining Neoaves, while analyses of non-coding data typically yield trees where Mirandornites (flamingos and grebes) is the sister of the remaining Neoaves. Our understanding of data type effects is hampered by the fact that previous analyses have used different taxa, loci, and types of non-coding data. Herein, we provide strong corroboration of the data type effects hypothesis for Neoaves by comparing trees based on coding and non-coding data derived from the same taxa and gene regions. A simple analytical method known to minimize biases due to base composition (coding nucleotides as purines and pyrimidines) resulted in coding exon data with increased congruence to the non-coding topology using concatenated analyses. These results improve our understanding of the resolution of neoavian phylogeny and point to a challenge—data type effects—that is likely to be an important factor in phylogenetic analyses of birds (and many other taxonomic groups). Using our results, we provide a summary phylogeny that identifies well-corroborated relationships and highlights specific nodes where future efforts should focus.

Phylogeny of hymenolepidids (Cestoda: Cyclophyllidea) from mammals: sequences of 18S rRNA and COI genes confirm major clades revealed by the 28S rRNA analyses

2021 ◽  
Vol 95 ◽  
Author(s):  
B. Neov ◽  
G.P. Vasileva ◽  
G. Radoslavov ◽  
P. Hristov ◽  
D.T.J. Littlewood ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
18S Rrna ◽  
Phylogenetic Analyses ◽  
The Other ◽  
Rrna Genes ◽  
Host Switching ◽  
28S Rrna ◽  
Mitochondrial Cytochrome ◽  
Rapid Radiation ◽  
18S Rrna Genes

Abstract The aim of the study is to test a hypothesis for the phylogenetic relationships among mammalian hymenolepidid tapeworms, based on partial (D1–D3) nuclear 28S ribosomal RNA (rRNA) genes, by estimating new molecular phylogenies for the group based on partial mitochondrial cytochrome c oxidase I (COI) and nuclear 18S rRNA genes, as well as a combined analysis using all three genes. New sequences of COI and 18S rRNA genes were obtained for Coronacanthus integrus, C. magnihamatus, C. omissus, C. vassilevi, Ditestolepis diaphana, Lineolepis scutigera, Spasskylepis ovaluteri, Staphylocystis tiara, S. furcata, S. uncinata, Vaucherilepis trichophorus and Neoskrjabinolepis sp. The phylogenetic analyses confirmed the major clades identified by Haukisalmi et al. (Zoologica Scripta 39: 631–641, 2010): Ditestolepis clade, Hymenolepis clade, Rodentolepis clade and Arostrilepis clade. While the Ditestolepis clade is associated with soricids, the structure of the other three clades suggests multiple evolutionary events of host switching between shrews and rodents. Two of the present analyses (18S rRNA and COI genes) show that the basal relationships of the four mammalian clades are branching at the same polytomy with several hymenolepidids from birds (both terrestrial and aquatic). This may indicate a rapid radiation of the group, with multiple events of colonizations of mammalian hosts by avian parasites.

Elusive Relationships Within Order Fabales: Phylogenetic Analyses Using matK and rbcL Sequence Data

2009 ◽  
Vol 34 (1) ◽  
pp. 102-114 ◽  
Author(s):  
M. A. Bello ◽  
A. Bruneau ◽  
F. Forest ◽  
J. A. Hawkins
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Evidence ◽  
Taxon Sampling ◽  
Rapid Radiation ◽  
Bayesian Approaches ◽  
Molecular Studies ◽  
Alternative Hypotheses ◽  
The One ◽  
Good Support

The order Fabales, including Leguminosae, Polygalaceae, Quillajaceae and Surianaceae, represents a novel hypothesis emerging from angiosperm molecular phylogenies. Despite good support for the order, molecular studies to date have suggested contradictory, poorly supported interfamilial relationships. Our reappraisal of relationships within Fabales addresses past taxon sampling deficiencies, and employs parsimony and Bayesian approaches using sequences from the plastid regions rbcL (166 spp.) and matK (78 spp.). Five alternative hypotheses for interfamilial relationships within Fabales were recovered. The Shimodaira-Hasegawa test found the likelihood of a resolved topology significantly higher than the one calculated for a polytomy, but did not favour any of the alternative hypotheses of relationship within Fabales. In the light of the morphological evidence available and the comparative behavior of rbcL and matK, the topology recovering Polygalaceae as sister to the rest of the order Fabales with Leguminosae more closely related to Quillajaceae + Surianaceae, is considered the most likely hypothesis of interfamilial relationships of the order. Dating of selected crown clades in the Fabales phylogeny using penalized likelihood suggests rapid radiation of the Leguminosae, Polygalaceae, and (Quillajaceae + Surianaceae) crown clades.

Hydraulic tomography using joint inversion of head and flux data 

2021 ◽  
Author(s):  
Behzad Pouladiborj ◽  
Olivier Bour ◽  
Niklas Linde ◽  
Laurent Longuevergne
Keyword(s):  
Hydraulic Conductivity ◽  
Joint Inversion ◽  
Data Type ◽  
Data Types ◽  
Hydraulic Tomography ◽  
Flux Data ◽  
Planning And Design ◽  
Constant Rate ◽  
Resolution Analysis ◽  
Constant Head

<p>Hydraulic tomography is a state of the art method for inferring hydraulic conductivity fields using head data. Here, a numerical model is used to simulate a steady-state hydraulic tomography experiment by assuming a Gaussian hydraulic conductivity field (also constant storativity) and generating the head and flux data in different observation points. We employed geostatistical inversion using head and flux data individually and jointly to better understand the relative merits of each data type. For the typical case of a small number of observation points, we find that flux data provide a better resolved hydraulic conductivity field compared to head data when considering data with similar signal-to-noise ratios. In the case of a high number of observation points, we find the estimated fields to be of similar quality regardless of the data type. A resolution analysis for a small number of observations reveals that head data averages over a broader region than flux data, and flux data can better resolve the hydraulic conductivity field than head data. The inversions' performance depends on borehole boundary conditions, with the best performing setting for flux data and head data are constant head and constant rate, respectively. However, the joint inversion results of both data types are insensitive to the borehole boundary type. Considering the same number of observations, the joint inversion of head and flux data does not offer advantages over individual inversions. By increasing the hydraulic conductivity field variance, we find that the resulting increased non-linearity makes it more challenging to recover high-quality estimates of the reference hydraulic conductivity field. Our findings would be useful for future planning and design of hydraulic tomography tests comprising the flux and head data.</p>

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