scholarly journals A Show of Character—a further response to Wiley et al.

Zootaxa ◽  
2011 ◽  
Vol 2946 (1) ◽  
pp. 29 ◽  
Author(s):  
ANTHONY C. GILL ◽  
RANDALL D. MOOI

Wiley et al. (2011) begin their critique of our paper (Mooi & Gill, 2010) with an assertion: “we need to make itclear that the foundation of their arguments rests not on scientific rigor, but rather on opinions about the re-classification of fishes using molecular data. This bias is the reason that they only targeted researchers who proposed changes in the higher-level taxonomy of fishes using phylogenetic hypotheses based on DNA sequence data (Miya et al. 2007, Smith & Craig 2007, Thacker 2009). In criticizing these studies, they do not suggest any alternative relationships or provide any counter evidence to the proposed relationships.” And on page 8, they apparently read our thoughts (aside from the title, none of the words in quotations was written by us in that context) and concluded: “Mooi & Gill entitled their paper “A crisis in fish systematics” because they long for the days when “real” ichthyologists found “meaningful” characters and “true” relationships.” Finally (p. 9), they contend that “Mooi & Gill’s various studies are usually focused on Johnson & Patterson’s (1993: 555) “disparate twigs of the [percomorph] tree,” whereas the explicit studies they criticize are large-scale and taxon rich datasets that have not otherwise been analyzed in Percomorpha.”

2007 ◽  
Vol 3 ◽  
pp. 193-197 ◽  
Author(s):  
Kou Amano ◽  
Hiroaki Ichikawa ◽  
Hidemitsu Nakamura ◽  
Hisataka Numa ◽  
Kaoru Fukami-Kobayashi ◽  
...  

Mycologia ◽  
2003 ◽  
Vol 95 (6) ◽  
pp. 1204 ◽  
Author(s):  
Laura Guzman-Davalos ◽  
Gregory M. Mueller ◽  
Joaquin Cifuentes ◽  
Andrew N. Miller ◽  
Anne Santerre

Phytotaxa ◽  
2018 ◽  
Vol 350 (1) ◽  
pp. 42 ◽  
Author(s):  
GALINA V. DEGTJAREVA ◽  
MICHAEL G. PIMENOV ◽  
TAHIR H. SAMIGULLIN

The systematic position of three Apiaceae-Apioideae taxa, Pinacantha porandica, Ladyginia bucharica and Peucedanum mogoltavicum, from Middle Asia and Afghanistan, is clarified based on nrITS DNA sequence data. In the molecular phylogenetic tree, the monotypic Pinacantha is placed in unresolved position within the Ferulinae. Although there is no morphological information on essential characters, we propose a new position of Pinacantha porandica within the genus Ferula. As a result a new combination Ferula porandica is proposed, with a new section Pinacantha to accommodate it. The attribution of Peucedanum mogoltavicum to Ferula has been confirmed, its correct name being Ferula lithophila. The genus Ladyginia should not be included in Ferula, its closest relatives being Mozaffariania and Glaucosciadium from the Glaucosciadium Clade.


1998 ◽  
Vol 11 (4) ◽  
pp. 631 ◽  
Author(s):  
Barbara G. Briggs

The 1996 Commemorative Proteaceae Conference drew attention to the large body of work proceeding on all southern continents, the extensive and informative fossil record, and the wide range of studies in ecology and reproductive biology. DNA sequence data and organogeny are producing major insights at the upper taxonomic levels, new phylogenetic hypotheses and classifications are emerging in respect of the recognition of subfamilies and the relationships and composition of tribes, and there is also evidence from morphology and DNA sequence data that several genera are paraphyletic.


2010 ◽  
Vol 23 (2) ◽  
pp. 69 ◽  
Author(s):  
Josephine Piggin ◽  
Jeremy J. Bruhl

Relationships between Callitris, Actinostrobus and Neocallitropsis, members of the southern hemisphere ‘callitroid clade’ (Callitroideae sensu Gadek et al. 2000) of Cupressaceae, are estimated using a database of 42 morphological and anatomical characters. Callitris is paraphyletic, with Actinostrobus being closer to a large well supported clade of 15 Australian species of Callitris than are C. baileyi, C. macleayana and the New Caledonian taxa. The New Caledonian unispecific endemic, Neocallitropsis, is sister to the clade comprising all Callitris and Actinostrobus species. There are marked differences between this estimate of the phylogeny and two recent estimates based on nuclear encoded DNA sequence data and non-molecular data, respectively, but some simlarities to the molecular estimate are highlighted and lead us here to formally include Actinostrobus within Callitris. Further molecular data are needed to test these results and explore the cause of the conflict between these estimates of the phylogeny within the group, and the status of Neocallitropsis.


2017 ◽  
Author(s):  
Erik Garrison ◽  
Jouni Sirén ◽  
Adam M. Novak ◽  
Glenn Hickey ◽  
Jordan M. Eizenga ◽  
...  

AbstractReference genomes guide our interpretation of DNA sequence data. However, conventional linear references are fundamentally limited in that they represent only one version of each locus, whereas the population may contain multiple variants. When the reference represents an individual’s genome poorly, it can impact read mapping and introduce bias. Variation graphs are bidirected DNA sequence graphs that compactly represent genetic variation, including large scale structural variation such as inversions and duplications.1 Equivalent structures are produced by de novo genome assemblers.2,3 Here we present vg, a toolkit of computational methods for creating, manipulating, and utilizing these structures as references at the scale of the human genome. vg provides an efficient approach to mapping reads onto arbitrary variation graphs using generalized compressed suffix arrays,4 with improved accuracy over alignment to a linear reference, creating data structures to support downstream variant calling and genotyping. These capabilities make using variation graphs as reference structures for DNA sequencing practical at the scale of vertebrate genomes, or at the topological complexity of new species assemblies.


Author(s):  
Thomas Stach ◽  
Samuel Dupont ◽  
Olle Israelson ◽  
Geraldine Fauville ◽  
Hiroaki Nakano ◽  
...  

The phylogenetic position of Xenoturbella spp. has been uncertain since their discovery in 1949. It has been recently suggested that they could be related to Ambulacraria within Deuterostomia. Ambulacraria is a taxon that has been suggested to consist of Hemichordata and Echinodermata. The hypothesis that X. bocki was related to Ambulacraria as well as the hypothesis of a monophyletic Ambulacraria is primarily based on the analysis of DNA sequence data. We tested both phylogenetic hypotheses using antibodies raised against SALMFamide 1 and 2 (S1, S2), neuropeptides isolated from echinoderms, on X. bocki and the enteropneust Harrimania kupfferi. Both species showed distinct positive immunoreactivity against S1 and S2. This finding supports the Ambulacraria-hypothesis and suggests a close phylogenetic relationship of X. bocki to Ambulacraria. In particular, the presence of immunoreactivity against S2 can be interpreted as a synapomorphy of Enteropneusta, Echinodermata, and Xenoturbella spp.


Nematology ◽  
2017 ◽  
Vol 19 (3) ◽  
pp. 351-374 ◽  
Author(s):  
Kerrie A. Davies ◽  
Weimin Ye ◽  
Barbara Center ◽  
Natsumi Kanzaki ◽  
Faerlie Bartholomaeus ◽  
...  

Aphelenchoidid nematodes were collected from the sycones ofFicussubgenusPharmacosyceafrom Central America. Two new species ofFicophaguswere recovered, and are described herein asF. maximasp. n. andF. yoponensissp. n. fromFicus maximaandF. yoponensis, respectively. They are differentiated from other species of the genus by a combination of morphological characters including having C-shaped females and spiral males, EP opening close to the lips, a short to long post-uterine sac, spicule characters, three pairs of subventral caudal papillae, DNA sequence data, biogeographical range, and host wasp andFicusspecies affiliation. The new species are differentiated from each other by spicule characters, length of the post-uterine sac, spermatheca shape, and female tail shape. In addition, three morphospecies were collected from sycones ofFicus glabrata,F. insipidaandF. tonduzii, respectively. Their morphological descriptions are presented but these taxa are not formally named as they currently lack molecular data.


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