Phylogeny and morphologic evolution of the Ordovician Camerata (Class Crinoidea, Phylum Echinodermata)

AbstractThe subclass Camerata (Crinoidea, Echinodermata) is a major group of Paleozoic crinoids that represents an early divergence in the evolutionary history and morphologic diversification of class Crinoidea, yet phylogenetic relationships among early camerates remain unresolved. This study conducted a series of quantitative phylogenetic analyses using parsimony methods to infer relationships of all well-preserved Ordovician camerate genera (52 taxa), establish the branching sequence of early camerates, and test the monophyly of traditionally recognized higher taxa, including orders Monobathrida and Diplobathrida. The first phylogenetic analysis identified a suitable outroup for rooting the Ordovician camerate tree and assessed affinities of the atypical dicyclic family Reteocrinidae. The second analysis inferred the phylogeny of all well-preserved Ordovician camerate genera. Inferred phylogenies confirm: (1) the Tremadocian genera Cnemecrinus and Eknomocrinus are sister to the Camerata; (2) as historically defined, orders Monobathrida and Diplobathrida do not represent monophyletic groups; (3) with minimal revision, Monobathrida and Diplobathrida can be re-diagnosed to represent monophyletic clades; (4) family Reteocrinidae is more closely related to camerates than to other crinoid groups currently recognized at the subclass level; and (5) several genera in subclass Camerata represent stem taxa that cannot be classified as either true monobathrids or true diplobathrids. The clade containing Monobathrida and Diplobathrida, as recognized herein, is termed Eucamerata to distinguish its constituent taxa from more basally positioned taxa, termed stem eucamerates. The results of this study provide a phylogenetic framework for revising camerate classification, elucidating patterns of morphologic evolution, and informing outgroup selection for future phylogenetic analyses of post-Ordovician camerates.

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Herpetological higher taxa nomina. 7. Lissamphibia Gadow, 1898

Bionomina ◽

10.11646/bionomina.21.1.4 ◽

2021 ◽

Vol 21 (1) ◽

pp. 73-83

Author(s):

ALAIN DUBOIS ◽

THIERRY FRÉTEY

Keyword(s):

Phylogenetic Relationships ◽

Rank Order ◽

Phylogenetic Analyses ◽

Higher Taxa ◽

The One

A taxon encompassing all recent taxa of amphibians and their close fossil relatives is highly supported as holophyletic in all recent phylogenetic analyses of amphibians. Under the Duplostensional Nomenclatural System, among twenty nomina available for this taxon, only one, Lissamphibia Gadow, 1898, qualifies as a sozodiaphonym and appears to be the one that should be used for this taxon, traditionally referred to the rank order. However, because of the current uncertainties in the phylogenetic relationships among basal amphibians, the allocation of this nomen to this taxon is still questionable. If it turned out to apply in fact to another, more comprehensive, taxon, its stabilisation under its current acceptation should be realised through an act of archoidy.

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Cretaceous origin and repeated tertiary diversification of the redefined butterflies

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2011.1430 ◽

2011 ◽

Vol 279 (1731) ◽

pp. 1093-1099 ◽

Cited By ~ 134

Author(s):

Maria Heikkilä ◽

Lauri Kaila ◽

Marko Mutanen ◽

Carlos Peña ◽

Niklas Wahlberg

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Relationships ◽

Evolutionary History ◽

Sister Group ◽

Morphological Characters ◽

Molecular Data ◽

Bayesian Approaches ◽

The Family ◽

Family Level ◽

Morphological And Molecular Data

Although the taxonomy of the ca 18 000 species of butterflies and skippers is well known, the family-level relationships are still debated. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the superfamilies Papilionoidea, Hesperioidea and Hedyloidea to date based on morphological and molecular data. We reconstructed their phylogenetic relationships using parsimony and Bayesian approaches. We estimated times and rates of diversification along lineages in order to reconstruct their evolutionary history. Our results suggest that the butterflies, as traditionally understood, are paraphyletic, with Papilionidae being the sister-group to Hesperioidea, Hedyloidea and all other butterflies. Hence, the families in the current three superfamilies should be placed in a single superfamily Papilionoidea. In addition, we find that Hedylidae is sister to Hesperiidae, and this novel relationship is supported by two morphological characters. The families diverged in the Early Cretaceous but diversified after the Cretaceous–Palaeogene event. The diversification of butterflies is characterized by a slow speciation rate in the lineage leading to Baronia brevicornis , a period of stasis by the skippers after divergence and a burst of diversification in the lineages leading to Nymphalidae, Riodinidae and Lycaenidae.

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A new concept for Dictyostelium sphaerocephalum based on morphology and phylogenetic analysis of nuclear ribosomal internal transcribed spacer region sequences

Canadian Journal of Botany ◽

10.1139/b06-147 ◽

2007 ◽

Vol 85 (1) ◽

pp. 104-110 ◽

Cited By ~ 2

Author(s):

Maria Romeralo ◽

Omar Fiz-Palacios ◽

Carlos Lado ◽

James C. Cavender

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Relationships ◽

Internal Transcribed Spacer ◽

Phylogenetic Analyses ◽

Morphological Plasticity ◽

Branching Pattern ◽

Classical Concept ◽

Internal Transcribed Spacer Region

Three dictyostelid isolates were found in Spain and Argentina that are morphologically different from known species. These isolates have some features similar to Dictyostelium sphaerocephalum (Oudem.) Sacc., Marchal & É.J. Marchal, but differ in size and sorocarp branching pattern. We sequenced the nuclear ribosomal internal transcribed spacer region to explore phylogenetic relationships among this group of species, including the three new isolates and their closest relatives. In all phylogenetic analyses performed, sequences of all three isolates group together with sequences from “typical” D. sphaerocephalum samples. This result supports previous observations of the morphological plasticity in dictyostelids, especially D. sphaerocephalum, leading us to broaden the classical concept of this species.

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The first-instar larva of the genus Arthropterus (Coleoptera : Carabidae : Paussinae): implications for evolution of myrmecophily and phylogenetic relationships within the subfamily

Invertebrate Systematics ◽

10.1071/is03028 ◽

2004 ◽

Vol 18 (2) ◽

pp. 101 ◽

Cited By ~ 11

Author(s):

Andrea Di Giulio ◽

Wendy Moore

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Relationships ◽

Sister Group ◽

Instar Larva ◽

First Instar ◽

Paraphyletic Group ◽

Phylogenetic Framework

The first-instar larva of the genus Arthropterus W.S. MacLeay, 1838 is described and illustrated. This is the first description of a newly hatched (first-instar) larva in the myrmecophilous tribe Paussini and the first known larva from a basal paussine lineage. A phylogenetic analysis of the subfamily based on larval characters confirms the placement of the genus Arthropterus as a sister-group of the remaining Paussini and supports the hypothesis that Metriini is the sister-group of Ozaenini+Paussini, with 'Ozaenini' as a paraphyletic group. Within this phylogenetic framework, we reassess which larval characters are diagnostic of the tribes Paussini and Ozaenini. Several larval features of Arthropterus, such as the riddled sensilla S-VIII and the fused terminal disk, are interpreted as adaptations to myrmecophily. This interpretation supports the hypothesis that larvae have played an important role in the evolution of myrmecophily within the subfamily Paussinae.

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Taxonomic scheme of the order Chaetophorales (Chlorophyceae, Chlorophyta) based on Chloroplast genomes

10.21203/rs.2.21773/v1 ◽

2020 ◽

Author(s):

Benwen Liu ◽

Yu Xin Hu ◽

Zheng Yu Hu ◽

Guo Xiang Liu ◽

Huan Zhu

Keyword(s):

Phylogenetic Analysis ◽

Chloroplast Genome ◽

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Genome Structure ◽

Genomic Analysis ◽

Comparative Genomic ◽

Rdna Sequences ◽

Chloroplast Genomes ◽

Basal Clade

Abstract Background Order Chaetophorales currently includes six families, namely Schizomeridaceae, Aphanochaetaceae, Barrancaceae, Uronemataceae, Fritschiellaceae, and Chaetophoraceae. Most studies have primarily focused on intergeneric phylogenetic relationships within this order and the phylogenetic relationships with four other Chlorophycean orders (Chaetophorales, Chaetopeltidales and Oedogoniales, and Volvocales). This study aimed to phylogenetically reconstruct order Chaetophorales and determine the taxonomic scheme and to further the current understanding of the evolution of order Chaetophorales. The taxonomic scheme of Chaetophorales has been inferred primarily through phylogenetic analysis based on rDNA sequences and phylogenetic relationships among families in order Chaetophorales remain unclear. Results In present study, seven complete and five fragmentary chloroplast genomes were harvested. Phylogenomic and comparative genomic analysis were performed to determine the taxonomic scheme within Chaetophorales. Consequently, Oedogoniales was found to be a sister to a clade linking Chaetophorales and Chaetopeltidales, Schizomeriaceae, and Aphanochaetaceae clustered into a well-resolved basal clade in Chaetophorales, inconsistent with the results of phylogenetic analysis based on rDNA sequences. Comparative genomic analyses revealed that the chloroplast genomes of Schizomeriaceae and Aphanochaetaceae were highly conserved and homologous, highlighting the closest relationship in this order. Germination types of zoospores precisely correlated with the phylogenetic relationships. Conclusions In conclusion, chloroplast genome structure analyses, synteny analyses, and zoospore germination analyses were concurrent with phylogenetic analyses based on the chloroplast genome, and all of them robustly determined the unique taxonomic scheme of Chaetophorales and the relationships of Oedogoniales, Chaetophorales, and Chaetopeltidales.

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Morphological reassessment and molecular assessment of Sargassum (Fucales: Phaeophyceae) species from the Gulf of California, Mexico

Phytotaxa ◽

10.11646/phytotaxa.183.4.1 ◽

2014 ◽

Vol 183 (4) ◽

pp. 201 ◽

Cited By ~ 3

Author(s):

GABRIELA ANDRADE-SORCIA ◽

RAFAEL RIOSMENA-RODRIGUEZ ◽

RAQUEL MUÑIZ-SALAZAR ◽

JUAN MANUEL LÓPEZ-VIVAS ◽

GA HUN BOO ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Relationships ◽

Brown Algae ◽

Gulf Of California ◽

Phylogenetic Analyses ◽

The Pacific ◽

Pacific Side ◽

Molecular Studies ◽

Molecular Assessment ◽

The Individual

Systematic molecular studies have not been performed on ecologically important brown algae (Sargassum) in the Gulf of California, Mexico, where 42 specific and infraspecific names have been recorded within this genus. We conducted phylogenetic analyses of nuclear ribosomal ITS and mitochondrial cox1 and cox3 sequences, along with detailed morphological observations of Sargassum collected in the Gulf of California. We confirmed the presence of six species, five previously described—S. herporhizum, S. horridum, S. johnstonii, S. lapazeanum, and S. sinicola, as well as the newly described Sargassum ulixei sp. nov. which is characterized by terete primary axes arising from the stipe, lanceolate to elliptical sessile ecostate blades with smooth margins, cryptostomata, ellipsoidal vesicles with a short mucron, and cylindrical to ellipsoidal receptacles. The individual analyses and subsequent phylogenetic analysis recognized two groups previously described by Dawson, one as Sargassum and other as Horridum. Our studies suggest that the Gulf of California is a region with endemic Sargassum species, and is clearly distinguished from the Pacific side of Baja California, where recently introduced species are common. Based on phylogenetic relationships, we propose two geographical origins for the Sargassum from the Gulf of California: a first group originating from the proto-Gulf, related to species from the northern hemisphere (including five species); and a second group, containing S. sinicola, introduced when the southern end opened at a later stage.

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HybPhaser: a workflow for the detection and phasing of hybrids in target capture datasets

10.1101/2020.10.27.354589 ◽

2020 ◽

Author(s):

Lars Nauheimer ◽

Nicholas Weigner ◽

Elizabeth Joyce ◽

Darren Crayn ◽

Charles Clarke ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Signal ◽

Phylogenetic Analyses ◽

List Type ◽

The Novel ◽

Paralogous Genes ◽

Target Capture ◽

Mapping Sequence ◽

Phylogenetic Framework ◽

Multiple References

AbstractPremise of the study: Hybrids contain divergent alleles that can confound phylogenetic analyses but can provide insights into parental lineages when identified and phased. We developed HybPhaser to detect hybrids in target capture datasets and to phase reads according to haplotypes based on similarity and a phylogenetic framework.Methods and Results: HybPhaser is an extension to the HybPiper sequence assembly workflow. We used Angiosperms353 target capture data for Nepenthes including known hybrids to test the novel workflow. Reference mapping was used to record heterozygous sites and identify hybrid accessions that were phased by mapping sequence reads to multiple references. The parental lineages of known hybrids were confirmed and conflicting phylogenetic signal reduced, improving the outcomes of phylogenetic analysis.Conclusions: HybPhaser is a novel pipeline for summarizing and optimizing target capture datasets, detecting hybrid accessions as well as paralogous genes, and generating phased accessions that can provide insights into reticulated evolution.

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Taxonomic scheme of the order Chaetophorales (Chlorophyceae, Chlorophyta) based on Chloroplast genomes

10.21203/rs.2.21773/v2 ◽

2020 ◽

Author(s):

Benwen Liu(Former Corresponding Author) ◽

Yu Xin Hu ◽

Zheng Yu Hu ◽

Guo Xiang Liu ◽

Huan Zhu(New Corresponding Author)

Keyword(s):

Phylogenetic Analysis ◽

Chloroplast Genome ◽

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Genome Structure ◽

Genomic Analysis ◽

Comparative Genomic ◽

Rdna Sequences ◽

Chloroplast Genomes ◽

Basal Clade

Abstract Background: Order Chaetophorales currently includes six families, namely Schizomeridaceae, Aphanochaetaceae, Barrancaceae, Uronemataceae, Fritschiellaceae, and Chaetophoraceae. The phylogenetic relationships of Chaetophorales have been inferred primarily through phylogenetic analysis based on rDNA sequences. Most studies have primarily focused on intergeneric phylogenetic relationships within this order and the phylogenetic relationships with four other Chlorophycean orders (Chaetophorales, Chaetopeltidales and Oedogoniales, and Volvocales). The phylogenetic relationships among families in order Chaetophorales remain unclear. This study aimed to phylogenetically reconstruct order Chaetophorales and determine the taxonomic scheme and to further the current understanding of the evolution of order Chaetophorales . Results: In the present study, seven complete and five fragmentary chloroplast genomes were harvested. Phylogenomic and comparative genomic analysis were performed to determine the taxonomic scheme within Chaetophorales. Consequently, Oedogoniales was found to be a sister to a clade linking Chaetophorales and Chaetopeltidales. Schizomeriaceae, and Aphanochaetaceae clustered into a well-resolved basal clade in Chaetophorales, inconsistent with the results of phylogenetic analysis based on rDNA sequences. Comparative genomic analyses revealed that the chloroplast genomes of Schizomeriaceae and Aphanochaetaceae were highly conserved and homologous, highlighting the closest relationship in this order. Germination types of zoospores precisely correlated with the phylogenetic relationships. Conclusions: chloroplast genome structure analyses, synteny analyses, and zoospore germination analyses were concurrent with phylogenetic analyses based on the chloroplast genome, and all of them robustly determined the unique taxonomic scheme of Chaetophorales and the relationships of Oedogoniales, Chaetophorales, and Chaetopeltidales.

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The evolutionary history of polycotylid plesiosaurians

Royal Society Open Science ◽

10.1098/rsos.172177 ◽

2018 ◽

Vol 5 (3) ◽

pp. 172177 ◽

Cited By ~ 11

Author(s):

V. Fischer ◽

R. B. J. Benson ◽

P. S. Druckenmiller ◽

H. F. Ketchum ◽

N. Bardet

Keyword(s):

Early Cretaceous ◽

Late Cretaceous ◽

Phylogenetic Relationships ◽

Evolutionary History ◽

Phylogenetic Analyses ◽

Neck Length ◽

Ecological Release ◽

Holotype Specimen ◽

Low Diversity ◽

History Of

Polycotylidae is a clade of plesiosaurians that appeared during the Early Cretaceous and became speciose and abundant early in the Late Cretaceous. However, this radiation is poorly understood. Thililua longicollis from the Middle Turonian of Morocco is an enigmatic taxon possessing an atypically long neck and, as originally reported, a series of unusual cranial features that cause unstable phylogenetic relationships for polycotylids. We reinterpret the holotype specimen of Thililua longicollis and clarify its cranial anatomy. Thililua longicollis possesses an extensive, foramina-bearing jugal, a premaxilla–parietal contact and carinated teeth. Phylogenetic analyses of a new cladistic dataset based on first-hand observation of most polycotylids recover Thililua and Mauriciosaurus as successive lineages at the base of the earliest Late Cretaceous polycotyline radiation. A new dataset summarizing the Bauplan of polycotylids reveals that their radiation produced an early burst of disparity during the Cenomanian–Turonian interval, with marked plasticity in relative neck length, but this did not arise as an ecological release following the extinction of ichthyosaurs and pliosaurids. This disparity vanished during and after the Turonian, which is consistent with a model of ‘early experimentation/late constraint’. Two polycotylid clades, Occultonectia clade nov. and Polycotylinae, survived up to the Maastrichtian, but with low diversity.

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Phylogenetic relationships among Elymus and related diploid genera (Triticeae: Poaceae) based on nuclear rDNA ITS sequences

Biologia ◽

10.1515/biolog-2015-0019 ◽

2015 ◽

Vol 70 (2) ◽

Cited By ~ 6

Author(s):

Gang Gao ◽

Jia-bin Deng ◽

Xue-mei Gou ◽

Qian Wang ◽

Chun-bang Ding ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Evolutionary History ◽

Phylogenetic Analyses ◽

Its Sequences ◽

Neighbor Joining ◽

Rdna Its ◽

Genome Donor ◽

Rdna Its Sequences ◽

History Of ◽

Elymus Species

AbstractTo investigate the phylogenetic relationships among Elymus and related diploid genera, the genome donor of Elymus, and the evolutionary history of polyploid Elymus species, nuclear ribosomal internal transcribed spacer (ITS) sequences were analyzed for 10 Elymus species, together with 17 diploid taxa from 5 monogenomic genera. The phylogenetic analyses (Neighbor-Joining) supported two major clades (St and H). Sequence diversity and genealogical analysis suggested that (1) Elymus species were unambiguously closely related to Pseudoroegeria; (2) Pse. stipifolia might be serve as the St genome donor of polyploid Elymus species; (3) the Y genome might be originated from ancestral lineage of Pseudoroegneria (St); (4) the ITS sequences of Elymus were evolutionarily distinct and may clarify parental lineages and phylogenetic relationships in Elymus.

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