scholarly journals Lack of support for Deuterostomia prompts reinterpretation of the first Bilateria

2021 ◽  
Vol 7 (12) ◽  
pp. eabe2741
Author(s):  
Paschalia Kapli ◽  
Paschalis Natsidis ◽  
Daniel J. Leite ◽  
Maximilian Fursman ◽  
Nadia Jeffrie ◽  
...  
Keyword(s):  
Systematic Error ◽  
Tree Reconstruction ◽  
Simulation Experiments ◽  
Animal Evolution ◽  
Phylogenetic Studies ◽  
Branch Lengths ◽  
Molecular Phylogenetic ◽  
Common Ancestors

The bilaterally symmetric animals (Bilateria) are considered to comprise two monophyletic groups, Protostomia (Ecdysozoa and the Lophotrochozoa) and Deuterostomia (Chordata and the Xenambulacraria). Recent molecular phylogenetic studies have not consistently supported deuterostome monophyly. Here, we compare support for Protostomia and Deuterostomia using multiple, independent phylogenomic datasets. As expected, Protostomia is always strongly supported, especially by longer and higher-quality genes. Support for Deuterostomia, however, is always equivocal and barely higher than support for paraphyletic alternatives. Conditions that cause tree reconstruction errors—inadequate models, short internal branches, faster evolving genes, and unequal branch lengths—coincide with support for monophyletic deuterostomes. Simulation experiments show that support for Deuterostomia could be explained by systematic error. The branch between bilaterian and deuterostome common ancestors is, at best, very short, supporting the idea that the bilaterian ancestor may have been deuterostome-like. Our findings have important implications for the understanding of early animal evolution.

scholarly journals Lack of support for Deuterostomia prompts reinterpretation of the first Bilateria

2020 ◽  
Author(s):  
Paschalia Kapli ◽  
Paschalis Natsidis ◽  
Daniel J. Leite ◽  
Maximilian Fursman ◽  
Nadia Jeffrie ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Tree Reconstruction ◽  
Simulation Experiments ◽  
Animal Evolution ◽  
Internal Branch ◽  
Embryonic Cleavage ◽  
Branch Lengths ◽  
Statistical Support ◽  
The Common ◽  
Molecular Characters

AbstractThe bilaterally symmetric animals (Bilateria) are considered to comprise two monophyletic groups, Protostomia and Deuterostomia. Protostomia contains the Ecdysozoa and the Lophotrochozoa; Deuterostomia contains the Chordata and the Xenambulacraria (Hemichordata, Echinodermata and Xenacoelomorpha). Their names refer to a supposed distinct origin of the mouth (stoma) in the two clades, but these groups have been differentiated by other embryological characters including embryonic cleavage patterns and different ways of forming their mesoderm and coeloms. Deuterostome monophyly is not consistently supported by recent studies. Here we compare support for Protostomia and Deuterostomia using five recently published, phylogenomic datasets. Protostomia is always strongly supported, especially by longer and higher quality genes. Support for Deuterostomia is always equivocal and barely higher than support for paraphyletic alternatives. Conditions that can cause tree reconstruction errors - inadequate models, short internal branch, faster evolving genes, and unequal branch lengths - correlate with statistical support for monophyletic deuterostomes. Simulation experiments show that support for Deuterostomia could be explained by systematic error. A survey of molecular characters supposedly diagnostic of deuterostomes shows many are not valid synapomorphies. The branch between bilaterian and deuterostome common ancestors, if real, is very short. This finding fits with growing evidence suggesting the common ancestor of all Bilateria had many deuterostome characteristics. This finding has important implications for our understanding of early animal evolution and for the interpretation of some enigmatic Cambrian fossils such as vetulicolians and banffiids.

Transfer of the Kobresia taxa of the flora of Russia and adjacent countries to the genus Carex (Cyperaceae)

2020 ◽  
pp. 125-129
Author(s):  
D. G. Melnikov ◽  
L. I. Krupkina
Keyword(s):  
International Collaboration ◽  
Morphological Characters ◽  
Published Data ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
New Nomenclatural Combinations

Based on the published data of molecular phylogenetic studies of the tribe Cariceae Dumort. genera (Cyperaceae), obtained by an international collaboration (The Global Carex Group, 2016; et al.), and morphological characters of the genera (Kukkonen, 1990; and others), new nomenclatural combinations and replacement names in the genus Carex L. are published for 11 species, one subspecies and two sections previously included in the genus Kobresia Willd.

Systematics and evolution of Lentibulariaceae: III. Utricularia

2018 ◽  
Author(s):  
Richard W. Jobson ◽  
Paulo C. Baleeiro ◽  
Cástor Guisande
Keyword(s):  
Gene Flow ◽  
Species Diversity ◽  
Population Level ◽  
Oceanic Islands ◽  
Vulnerable Species ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic

Utricularia is a morphologically and ecologically diverse genus currently comprising more than 230 species divided into three subgenera—Polypompholyx, Utricularia, and Bivalvaria—and 35 sections. The genus is distributed worldwide except on the poles and most oceanic islands. The Neotropics has the highest species diversity, followed by Australia. Compared to its sister genera, Utricularia has undergone greater rates of speciation, which are linked to its extreme morphological flexibility that has resulted in the evolution of habitat-specific forms: terrestrial, rheophytic, aquatic, lithophytic, and epiphytic. Molecular phylogenetic studies have resolved relationships for 44% of the species across 80% of the sections. Scant data are available for phylogeography or population-level processes such as gene flow, hybridization, or pollination. Because nearly 90% of the species are endemics, data are urgently needed to determine how to protect vulnerable species and their habitats.

Paracarphalea, a new genus of the coffee family segregated from the Malagasy endemic genus Carphalea (Rubiaceae, Rubioideae, Knoxieae)

Phytotaxa ◽  
2016 ◽  
Vol 263 (2) ◽  
pp. 98 ◽  
Author(s):  
JULIA FERM ◽  
JESPER KÅREHED ◽  
BIRGITTA BREMER ◽  
SYLVAIN G. RAZAFIMANDIMBISON
Keyword(s):  
Bayesian Methods ◽  
Type Species ◽  
New Genus ◽  
Sequence Data ◽  
Conservation Status ◽  
Endemic Genus ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
Nuclear Its ◽  
Iucn Criteria

The Malagasy genus Carphalea (Rubiaceae) consists of six species (C. angulata, C. cloiselii, C. kirondron, C. linearifolia, C. madagascariensis, C. pervilleana) of shrubs or small trees and is recognizable by a distinctly lobed calyx, 2(–4)-locular ovaries, each locule with several ovules on a rod-like stalk arising from the base of the locule, and indehiscent fruits. Carphalea linearifolia, rediscovered in 2010, has not previously been included in any Rubiaceae molecular phylogenetic studies. We re-investigated the monophyly of Carphalea using sequence data from chloroplast (rps16 and trnT-F) and nuclear (ITS and ETS) markers analysed with parsimony and Bayesian methods. Carphalea linearifolia forms a clade with C. cloiselii and the type species C. madagascariensis. This clade is sister to a clade consisting of the rest of the Carphalea species plus the genus Triainolepis. According to these results, the new genus Paracarphalea is here described to accommodate Carphalea angulata, C. kirondron, and C. pervilleana. The conservation status of Carphalea linearifolia is assessed as critically endangered according to IUCN criteria.

scholarly journals Notes on Some Interesting Sporocarp-Inhabiting Fungi Isolated from Xylarialean Fungi in Japan

Diversity ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 574
Author(s):  
Wasiatus Sa’diyah ◽  
Akira Hashimoto ◽  
Gen Okada ◽  
Moriya Ohkuma
Keyword(s):  
Dry Forest ◽  
Trichoderma Spp ◽  
Factors Affecting ◽  
Phylogenetic Studies ◽  
Moist Forest ◽  
Mycoparasitic Fungi ◽  
Molecular Phylogenetic ◽  
Ibaraki Prefecture ◽  
Soil Borne Fungi ◽  
Isolated Species

The diversity of sporocarp-inhabiting fungi (SCIF) was examined using six samples of xylarialean fungi from two different forests in Ibaraki Prefecture, Japan: a moist forest in the Sakuragawa area and an urban dry forest in the Tsukuba area. These fungi were enumerated using direct observation and dilution plate methods. We obtained 44 isolates, and careful morphological and molecular phylogenetic studies of these isolates revealed that approximately 30% of the operating taxonomic units were undescribed or cryptic species related to known fungi. Although typical mycoparasitic fungi, such as helotialean fungi and Trichoderma spp., were not isolated, the genera Acremonium, Acrodontium, and Simplicillium were detected. Comparisons of SCIF communities between the two forests suggested that the number of isolated species in the Sakuragawa area was lower than that in the Tsukuba area. Soil-borne fungi, such as Aspergillus, Beauveria, Penicillium, and Talaromyces, or polypores/corticioid mushrooms, are frequently detected in the Tsukuba area. Factors affecting SCIF communities in the two forests are discussed. Some noteworthy fungi are briefly described with notes on taxonomy, ecology, and molecular phylogeny.

scholarly journals Fungi of entomopathogenic potential in Chytridiomycota and Blastocladiomycota, and in fungal allies of the Oomycota and Microsporidia

IMA Fungus ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Agata Kaczmarek ◽  
Mieczysława I. Boguś
Keyword(s):  
Biological Control Agent ◽  
Sister Group ◽  
Control Agent ◽  
Scale Insects ◽  
Black Flies ◽  
Larval Stages ◽  
Phylogenetic Studies ◽  
Lady Beetles ◽  
Molecular Phylogenetic ◽  
The Relationship

AbstractThe relationship between entomopathogenic fungi and their insect hosts is a classic example of the co-evolutionary arms race between pathogen and target host. The present review describes the entomopathogenic potential of Chytridiomycota and Blastocladiomycota fungi, and two groups of fungal allies: Oomycota and Microsporidia. The Oomycota (water moulds) are considered as a model biological control agent of mosquito larvae. Due to their shared ecological and morphological similarities, they had long been considered a part of the fungal kingdom; however, phylogenetic studies have since placed this group within the Straminipila. The Microsporidia are parasites of economically-important insects, including grasshoppers, lady beetles, bumblebees, colorado potato beetles and honeybees. They have been found to display some fungal characteristics, and phylogenetic studies suggest that they are related to fungi, either as a basal branch or sister group. The Blastocladiomycota and Chytridiomycota, named the lower fungi, historically were described together; however, molecular phylogenetic and ultrastructural research has classified them in their own phylum. They are considered parasites of ants, and of the larval stages of black flies, mosquitoes and scale insects.

scholarly journals A phylogenetic analysis of the genus Pleurothallis, with emphasis on Pleurothallis subsection Macrophyllae-Fasciculatae, using nuclear ITS and chloroplast DNA sequencing

Lankesteriana ◽  
2011 ◽  
Vol 11 (3) ◽  
Author(s):  
M. Wilson ◽  
C. Belle ◽  
A. Dang ◽  
P. Hannan ◽  
C. Kenyon ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Preliminary Data ◽  
Plastid Dna ◽  
Maximum Parsimony Tree ◽  
Its Sequencing ◽  
Phylogenetic Studies ◽  
Parsimony Tree ◽  
Molecular Phylogenetic ◽  
Nuclear Its ◽  
Expanded Concept

Several revisions of the genus Pleurothallis have been proposed. Luer has proposed that Pleurothallis species in subgenus Scopula be segregated into the genera Colombiana and Ancipitia. Szlachetko and Margonska (2001) proposed the genus Zosterophyllanthos for Pleurothallis subsection Macrophyllae-Fasciculatae. As an alternative, Luer (2005) proposed the genus Acronia by uniting Pleurothallis subsection Macrophyllae-Fasciculatae with subsections Acroniae and Amphygiae. The molecular phylogenetic studies by Pridgeon and Chase (2001), however, suggested that these taxonomic revisions might not be justified. We report here a more detailed phylogenetic analysis of the genus Pleurothallis, with emphasis on subsection Macrophyllae-Fasciculatae, with data primarily from nuclear ITS sequencing, supplemented with preliminary data from plastid DNA (rpoB2, rpoC1, and ycf1) sequencing. Some initial, tentative conclusions can be drawn. In the strict consensus maximum-parsimony tree of ITS data, many of the clades collapse, leaving a polytomy with a single, highly supported node that tentatively could be used to delimit the genus Pleurothallis. Such a tree would argue for an expanded concept of the genus Pleurothallis, in which the groups Ancipitia, Colombiana, and Acronia/Zosterophyllanthos, if shown to be monophyletic, are relegated to subgenera. 

The phylogenetic position of the enigmatic Assam day gecko Cnemaspis cf. assamensis (Squamata: Gekkonidae) demonstrates a novel biogeographic connection between Northeast India and south India-Sri Lanka

2021 ◽  
pp. 1-13
Author(s):  
Ishan Agarwal ◽  
Rachunliu G. Kamei ◽  
Stephen Mahony
Keyword(s):  
Sri Lanka ◽  
Southeast Asia ◽  
South Asian ◽  
South India ◽  
Northeast India ◽  
Phylogenetic Position ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
Nd2 Gene ◽  
Isolated Species

Abstract Northeast Indian biodiversity has long been considered to have a stronger affinity to Southeast Asian rather than Peninsular Indian fauna, however, few molecular phylogenetic studies have explored this hypothesis. In Asia, the polyphyletic gekkonid genus Cnemaspis sensu lato is comprised of two distantly related groups; one primarily from South Asia with some members in Southeast Asia, and the other exclusively from Southeast Asia. Cnemaspis assamensis is a systematically obscure and geographically isolated species (>1400 km from its nearest congeners) from the Brahmaputra River Valley in Northeast India. We provide the first molecular phylogenetic assessment of this species based on a partial ND2 gene fragment. Cnemaspis assamensis is determined to be a deeply divergent (Oligocene) member of the South Asian radiation and is sister to the podihuna clade which is endemic to Sri Lanka. The biogeographic implications of this find are discussed and this is suspected to represent a rare example of true disjunction between the wet zones of Northeast India and southern India/Sri Lanka. These results further emphasise the importance of Northeast India as a refuge for unique ancient faunal lineages.

scholarly journals Semiaquilegia danxiashanensis (Ranunculaceae), a new species from Danxia Shan in Guangdong, southern China

Phytotaxa ◽  
2019 ◽  
Vol 405 (1) ◽  
pp. 1 ◽  
Author(s):  
JIAN-JUN ZHOU ◽  
ZHANG-PING HUANG ◽  
JIA-HUI LI ◽  
SCOTT HODGES ◽  
WEI-SHENG DENG ◽  
...  
Keyword(s):  
New Species ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Separate Species ◽  
F Region ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
Nuclear Its ◽  
A New Species ◽  
Northern Guangdong

Based on morphological and molecular phylogenetic studies, Semiaquilegia danxiashanensis, a new species from Danxia Shan in northern Guangdong, southern China, is described and illustrated. This species is easily distinguishable from each of other three known species in the genus by characters of the flowers and fruits. In addition, molecular phylogenetic analyses of both the nuclear ITS and the plastid trnL-F region strongly supported S. danxiashanensis as a separate species from other species of Semiaquilegia. We provide a detailed morphological and habitat description, distribution, as well as colour photographs and illustrations of the new species.

scholarly journals Phylogenomic analysis of echinoderm class relationships supports Asterozoa

2014 ◽  
Vol 281 (1786) ◽  
pp. 20140479 ◽  
Author(s):  
Maximilian J. Telford ◽  
Christopher J. Lowe ◽  
Christopher B. Cameron ◽  
Olga Ortega-Martinez ◽  
Jochanan Aronowicz ◽  
...  
Keyword(s):  
Convergent Evolution ◽  
Sea Urchins ◽  
Phylogenetic Signal ◽  
Strong Support ◽  
Phylogenomic Analysis ◽  
Phylogenetic Studies ◽  
Phylogenetic Methods ◽  
Complete Dataset ◽  
Type Larva ◽  
Molecular Phylogenetic

While some aspects of the phylogeny of the five living echinoderm classes are clear, the position of the ophiuroids (brittlestars) relative to asteroids (starfish), echinoids (sea urchins) and holothurians (sea cucumbers) is controversial. Ophiuroids have a pluteus-type larva in common with echinoids giving some support to an ophiuroid/echinoid/holothurian clade named Cryptosyringida. Most molecular phylogenetic studies, however, support an ophiuroid/asteroid clade (Asterozoa) implying either convergent evolution of the pluteus or reversals to an auricularia-type larva in asteroids and holothurians. A recent study of 10 genes from four of the five echinoderm classes used ‘phylogenetic signal dissection’ to separate alignment positions into subsets of (i) suboptimal, heterogeneously evolving sites (invariant plus rapidly changing) and (ii) the remaining optimal, homogeneously evolving sites. Along with most previous molecular phylogenetic studies, their set of heterogeneous sites, expected to be more prone to systematic error, support Asterozoa. The homogeneous sites, in contrast, support an ophiuroid/echinoid grouping, consistent with the cryptosyringid clade, leading them to posit homology of the ophiopluteus and echinopluteus. Our new dataset comprises 219 genes from all echinoderm classes; analyses using probabilistic Bayesian phylogenetic methods strongly support Asterozoa. The most reliable, slowly evolving quartile of genes also gives highest support for Asterozoa; this support diminishes in second and third quartiles and the fastest changing quartile places the ophiuroids close to the root. Using phylogenetic signal dissection, we find heterogenous sites support an unlikely grouping of Ophiuroidea + Holothuria while homogeneous sites again strongly support Asterozoa. Our large and taxonomically complete dataset finds no support for the cryptosyringid hypothesis; in showing strong support for the Asterozoa, our preferred topology leaves the question of homology of pluteus larvae open.

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