Phylogenetic relationships of extant echinoderm classes

2001 ◽  
Vol 79 (7) ◽  
pp. 1232-1250 ◽  
Author(s):  
Daniel Janies
Keyword(s):  
Phylogenetic Relationships ◽  
Sea Urchins ◽  
Strong Support ◽  
Sensitivity Analyses ◽  
Molecular Evidence ◽  
Evolutionary Models ◽  
Sea Cucumbers ◽  
Computational Approaches ◽  
Evidential Value ◽  
Nuclear Loci

A well-supported phylogeny of echinoderm classes has eluded morphological, embryological, molecular, and combined analyses. From this body of work it is apparent that (i) echinoids (sea urchins) and holothuroids (sea cucumbers) are related, and (ii) crinoids (sea lilies) are the sister taxon to extant eleutherozoan classes (asteroids, ophiuroids, echinoids, and holothuroids). However, the relationships of asteroids and ophiuroids to other echinoderm classes have been difficult to recover. To address relationships between the asteroids and ophiuroids and other echinoderms, I have sequenced additional nuclear loci and taxa and used novel computational approaches for co-optimizing morphological with molecular evidence at the level of sequence alignment. Support for the monophyly of each class is strong. Support for a monophyletic Asteroidea + Xyloplax is as strong as for Asteroidea. Support for Asterozoa (Asteroidea + Ophiuroidea) is apparent, albeit not as strong as for other clades (e.g., Echinozoa, Eleutherozoa, and Echinodermata). I also present detailed sensitivity analyses to provide (i) a test of the monophyly of groups under a variety of evolutionary models and (ii) a statement of the evidential value of various character systems.

Phylogenetic relationships in Hypomyces and allied genera, with emphasis on species growing on wood-decaying homobasidiomycetes

2000 ◽  
Vol 77 (12) ◽  
pp. 1756-1768 ◽  
Author(s):  
Kadri Põldmaa ◽  
Ellen Larsson ◽  
Urmas Kõljalg
Keyword(s):  
Maximum Likelihood ◽  
Sexual Reproduction ◽  
Phylogenetic Relationships ◽  
New Genus ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Sister Group ◽  
28S Rdna ◽  
The Other ◽  
Molecular Evidence

To infer phylogenetic relationships among species of Hypomyces (Fr.) Tul and allied genera, partial sequences of the 28S rDNA were obtained for 21 strains representing 19 species. On the basis of these data and 38 sequences obtained from GenBank, phylogenetic analyses were performed using the programs PAUP and Pee-Wee. Hypomyces appears to be paraphyletic, with species having wet-conidial phialidic anamorphs more closely related to other genera. Hypomyces chrysostomus Berk & Broome is a sister group to the clade that includes species of Aphysiostroma Barrasa et al., Arachnocrea Moravec, and Hypocrea Fr. Based on morphological and molecular evidence, a new genus, Sporophagomyces, is described for Hypomyces chrysostomus and two allied species. Hypomyces broomeanus Tul. forms one clade with species of Sphaerostilbella Sacc. and is transferred to this genus. The recognition of Arachnocrea is justified. The integration of Cladobotryum Nees species that are not known to undergo sexual reproduction with Hypomyces species that possess Cladobotryum anamorphs receives strong support, but the whole complex of these species appears to be paraphyletic. However, constraint trees, which require monophyly of all these ana- and pleo-morphic species, do not appear significantly less likely than the other trees obtained under maximum likelihood or parsimony criteria. For the remaining species of Hypomyces, four distinct lineages are distinguished.

The sterols of echinoderms

1972 ◽  
Vol 180 (1059) ◽  
pp. 223-246 ◽  
Keyword(s):  
Phylogenetic Relationships ◽  
Marine Invertebrates ◽  
Sea Urchins ◽  
Point Of View ◽  
Biological Origin ◽  
Sea Cucumbers ◽  
Biochemical Evidence ◽  
Modern Methods ◽  
Close Relationship ◽  
The One

The pioneering work of Bergmann and his colleagues demonstrated that marine invertebrates in many cases contain complex sterol mixtures consisting of C 27 , C 28 and C 29 sterols of varying degrees of unsaturation (Bergmann 1949, 1962). The sterols found in the phylum Echinodermata have proved of particular interest not only from the point of view of their composition and biological origin but also from phylogenetic considerations. Dorée (1909) first recognized that the sterol of a starfish differed from cholesterol, the typical sterol of higher animals. Later Kossel & Edlbacher (1915) obtained the sterol from a starfish, Asteropecten aurantiacus , and named it stellasterol. Subsequently Bergmann & Stansbury (1944) concluded that starfish sterols are mixtures which include stellastenol (1) and stellasterol, the 22, 23-dihydro derative of stellastenol (Shoppee 1964) Extending their studies Bergmann and co-workers demonstrated that the echinoderms can be divided into two groups on the basis of the types of sterol which they contain. Crinoidea (sea lilies), Ophiuroidea (brittle stars) and Echinoidea (sea urchins) contain sterols with a ∆ 5 bond while the Asteroidea (starfish) and Holothuroidea (sea cucumbers) contain mixtures in which sterols with a ∆ 7 bond predominate (Bergmann 1962). This division of echinoderms according to sterol type has recently been confirmed by Gupta & Scheuer (1968) using more modern methods of sterol analysis. Bergmann (1962) concluded that the distribution of ∆ 5 and ∆ 7 sterols in the different classes of echinoderms is a reflexion of the phylogenetic relationships which exist in the phylum. From embryological evidence there is a close relationship between the asteroids and holothuroids on the one hand and the ophiuroids and echinoids on the other (Bergmann 1962; Hyman 1955). In addition to the data on sterols other comparative biochemical evidence on the occurrence and distribution of batyl alcohol, spinochromes and phosphagens in echinoderms is in accord with these phylogenetic relationships (Singh, Moore & Scheuer 1967; Bolker 1967 α ). The validity of the embryological and biochemical evidence, however, has been contested by Fell who regards the asteroids to be more closely related to the ophiuroids while the holothuroids have some affinities with the echinoids (Fell 1948, 1963, 1965; Fell & Pawson 1966; Bolker 1967 α ).

scholarly journals Two Complete Mitochondrial Genomes of Mileewinae (Hemiptera: Cicadellidae) and a Phylogenetic Analysis

Insects ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 668
Author(s):  
Tinghao Yu ◽  
Yalin Zhang
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Strong Support ◽  
Intergenic Spacer ◽  
Taxonomic Status ◽  
Start Codon ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Protein Coding

More studies are using mitochondrial genomes of insects to explore the sequence variability, evolutionary traits, monophyly of groups and phylogenetic relationships. Controversies remain on the classification of the Mileewinae and the phylogenetic relationships between Mileewinae and other subfamilies remain ambiguous. In this study, we present two newly completed mitogenomes of Mileewinae (Mileewa rufivena Cai and Kuoh 1997 and Ujna puerana Yang and Meng 2010) and conduct comparative mitogenomic analyses based on several different factors. These species have quite similar features, including their nucleotide content, codon usage of protein genes and the secondary structure of tRNA. Gene arrangement is identical and conserved, the same as the putative ancestral pattern of insects. All protein-coding genes of U. puerana began with the start codon ATN, while 5 Mileewa species had the abnormal initiation codon TTG in ND5 and ATP8. Moreover, M. rufivena had an intergenic spacer of 17 bp that could not be found in other mileewine species. Phylogenetic analysis based on three datasets (PCG123, PCG12 and AA) with two methods (maximum likelihood and Bayesian inference) recovered the Mileewinae as a monophyletic group with strong support values. All results in our study indicate that Mileewinae has a closer phylogenetic relationship to Typhlocybinae compared to Cicadellinae. Additionally, six species within Mileewini revealed the relationship (U. puerana + (M. ponta + (M. rufivena + M. alara) + (M. albovittata + M. margheritae))) in most of our phylogenetic trees. These results contribute to the study of the taxonomic status and phylogenetic relationships of Mileewinae.

Molecular evidence for phylogenetic relationships among buntings and American sparrows (Emberizidae)

2001 ◽  
Vol 32 (2) ◽  
pp. 95-101 ◽  
Author(s):  
Alessandro Grapputo ◽  
Andrea Pilastro ◽  
Allan J. Baker ◽  
Guglielmo Marin
Keyword(s):  
Phylogenetic Relationships ◽  
Molecular Evidence

scholarly journals Phylogenetic Position of the New World Quail (Odontophoridae): Eight Nuclear Loci and Three Mitochondrial Regions Contradict Morphology and the Sibley-Ahlquist Tapestry

The Auk ◽  
2007 ◽  
Vol 124 (1) ◽  
pp. 71-84 ◽  
Author(s):  
W. Andrew Cox ◽  
Rebecca T. Kimball ◽  
Edward L. Braun
Keyword(s):  
New World ◽  
Sequence Data ◽  
Evolutionary Relationship ◽  
Strong Support ◽  
Nuclear Data ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Data Set ◽  
Mitochondrial Data ◽  
Nuclear Loci

Abstract The evolutionary relationship between the New World quail (Odontophoridae) and other groups of Galliformes has been an area of debate. In particular, the relationship between the New World quail and guineafowl (Numidinae) has been difficult to resolve. We analyzed >8 kb of DNA sequence data from 16 taxa that represent all major lineages of Galliformes to resolve the phylogenetic position of New World quail. A combined data set of eight nuclear loci and three mitochondrial regions analyzed with maximum parsimony, maximum likelihood, and Bayesian methods provide congruent and strong support for New World quail being basal members of a phasianid clade that excludes guineafowl. By contrast, the three mitochondrial regions exhibit modest incongruence with each other. This is reflected in the combined mitochondrial analyses that weakly support the Sibley-Ahlquist topology that placed the New World quail basal in relation to guineafowl and led to the placement of New World quail in its own family, sister to the Phasianidae. However, simulation-based topology tests using the mitochondrial data were unable to reject the topology suggested by our combined (mitochondrial and nuclear) data set. By contrast, similar tests using our most likely topology and our combined nuclear and mitochondrial data allow us to strongly reject the Sibley-Ahlquist topology and a topology based on morphological data that unites Old and New World quail. Posición Filogenética de las Codornices del Nuevo Mundo (Odontophoridae): Ocho Loci Nucleares y Tres Regiones Mitocondriales Contradicen la Morfología y la Filogenia de Sibley y Ahlquist

scholarly journals Meta-Analytic Findings in the Self-Controlled Motor Learning Literature: Underpowered, Biased, and Lacking Evidential Value

2021 ◽  
Author(s):  
Brad McKay ◽  
Zachary Yantha ◽  
Julia Hussien ◽  
Michael J Carter ◽  
Diane M. Ste-Marie
Keyword(s):  
Motor Learning ◽  
Weight Function ◽  
Selection Bias ◽  
The Self ◽  
Sensitivity Analyses ◽  
P Value ◽  
Function Model ◽  
Evidential Value ◽  
Significant Difference ◽  
The Impact

The self-controlled motor learning literature consists of experiments that compare a group of learners who are provided with a choice over an aspect of their practice environment to a group who are yoked to those choices. A qualitative review of the literature suggests an unambiguous benefit from self-controlled practice. A meta-analysis was conducted on the effects of self-controlled practice on retention test performance measures with a focus on assessing and potentially correcting for selection bias in the literature, such as publication bias and p-hacking. First, a naïve random effects model was fit to the data and a moderate benefit of self-controlled practice, g=.44 (k= 52,N= 3134,95%CI[.31, .56]), was found. Second, publication status was added to the model as a potential moderator, revealing a significant difference between published and unpublished findings, with only the former reporting a benefit of self-controlled practice. Third, to investigate and adjust for the impact of selectively reporting statistically significant results, a weight-function model was fit to the data with a one-tailed p-value cutpoint of .025. The weight-function model revealed substantial selection bias and estimated the true average effect of self-controlled practice as g=.107 (95%CI[.047, .18]). P-curve analyses were conducted on the statistically significant results published in the literature and the outcome suggested a lack of evidential value. Fourth, a suite of sensitivity analyses were conducted to evaluate the robustness of these results, all of which converged on trivially small effect estimates. Overall, our results suggest the benefit of self-controlled practice on motor learning is small and not currently distinguishable from zero.

Phylogenetic relationships in the monocot order Commelinales, with a focus on PhilydraceaeThis paper is one of a selection of papers published in the Special Issue on Systematics Research.

Botany ◽  
2008 ◽  
Vol 86 (7) ◽  
pp. 719-731 ◽  
Author(s):  
Jeffery M. Saarela ◽  
Peter J. Prentis ◽  
Hardeep S. Rai ◽  
Sean W. Graham
Keyword(s):  
Phylogenetic Relationships ◽  
Strong Support ◽  
Sister Group ◽  
Higher Order ◽  
Special Issue ◽  
Likelihood Methods ◽  
The Family ◽  
Selection Of

To characterize higher-order phylogenetic relationships among the five families of Commelinales, we surveyed multiple plastid loci from exemplar taxa sampled broadly from the order, and from other major monocot lineages. Phylogenetic inferences in Commelinales using parsimony and likelihood methods are congruent, and we find strong support for most aspects of higher-order relationship in the order. We obtain moderately strong support for the local placement of Philydraceae, a family whose position has proven particularly difficult to infer in previous studies. Commelinaceae and Hanguanaceae are sister taxa, and together they are the sister group of a clade consisting of Haemodoraceae, Philydraceae, and Pontederiaceae; Haemodoraceae and Pontederiaceae are also sister taxa. Our sampling of Philydraceae includes all three or four genera in the family; we identify Philydrella as the sister group of a Helmholtzia–Philydrum clade, a resolution that is potentially consistent with several aspects of morphology.

Phylogeny of the Styracaceae Revisited Based on Whole Plastome Sequences, Including Novel Plastome Data from Parastyrax

2021 ◽  
Vol 46 (1) ◽  
pp. 162-174
Author(s):  
Ming-Hui Yan ◽  
Chun-Yang Li ◽  
Peter W. Fritsch ◽  
Jie Cai ◽  
Heng-Chang Wang
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Signal ◽  
Strong Support ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
The Family ◽  
Small Single Copy

Abstract—The phylogenetic relationships among 11 out of the 12 genera of the angiosperm family Styracaceae have been largely resolved with DNA sequence data based on all protein-coding genes of the plastome. The only genus that has not been phylogenomically investigated in the family with molecular data is the monotypic genus Parastyrax, which is extremely rare in the wild and difficult to collect. To complete the sampling of the genera comprising the Styracaceae, examine the plastome composition of Parastyrax, and further explore the phylogenetic relationships of the entire family, we sequenced the whole plastome of P. lacei and incorporated it into the Styracaceae dataset for phylogenetic analysis. Similar to most others in the family, the plastome is 158189 bp in length and contains a large single-copy region of 88085 bp and a small single-copy region of 18540 bp separated by two inverted-repeat regions of 25781 bp each. A total of 113 genes was predicted, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic relationships among all 12 genera of the family were constructed with 79 protein-coding genes. Consistent with a previous study, Styrax, Huodendron, and a clade of Alniphyllum + Bruinsmia were successively sister to the remainder of the family. Parastyrax was strongly supported as sister to an internal clade comprising seven other genera of the family, whereas Halesia and Pterostyrax were both recovered as polyphyletic, as in prior studies. However, when we employed either the whole plastome or the large- or small-single copy regions as datasets, Pterostyrax was resolved as monophyletic with 100% support, consistent with expectations based on morphology and indicating that non-coding regions of the Styracaceae plastome contain informative phylogenetic signal. Conversely Halesia was still resolved as polyphyletic but with novel strong support.

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