scholarly journals Exploring phylogenomic relationships within Myriapoda: should high matrix occupancy be the goal?

2015 ◽  
Author(s):  
Rosa Fernandez ◽  
Gregory D Edgecombe ◽  
Gonzalo Giribet
Keyword(s):  
Sister Group ◽  
Molecular Data ◽  
Taxon Sampling ◽  
Molecular Evidence ◽  
Data Sets ◽  
The Family ◽  
Family Level ◽  
Conserved Genes ◽  
Bayesian Mixture ◽  
Bayesian Mixture Models

Myriapods are one of the dominant terrestrial arthropod groups including the diverse and familiar centipedes and millipedes. Although molecular evidence has shown that Myriapoda is monophyletic, its internal phylogeny remains contentious and understudied, especially when compared to those of Chelicerata and Hexapoda. Until now, efforts have focused on taxon sampling (e.g., by including a handful of genes in many species) or on maximizing matrix occupancy (e.g., by including hundreds or thousands of genes in just a few species), but a phylogeny maximizing sampling at both levels remains elusive. In this study, we analyzed forty Illumina transcriptomes representing three myriapod classes (Diplopoda, Chilopoda and Symphyla); twenty-five transcriptomes were newly sequenced to maximize representation at the ordinal level in Diplopoda and at the family level in Chilopoda. Eight supermatrices were constructed to explore the effect of several potential phylogenetic biases (e.g., rate of evolution, heterotachy) at three levels of mean gene occupancy per taxon (50%, 75% and 90%). Analyses based on maximum likelihood and Bayesian mixture models retrieved monophyly of each myriapod class, and resulted in two alternative phylogenetic positions for Symphyla, as sister group to Diplopoda + Chilopoda, or closer to Diplopoda, the latter hypothesis having been traditionally supported by morphology. Within centipedes, all orders were well supported, but two nodes remained in conflict in the different analyses despite dense taxon sampling at the family level, situating the order Scolopendromorpha as sister group to a morphologically-anomalous grouping of Lithobiomorpha + Geophilomorpha in a subset of analyses. Interestingly, this anomalous result was obtained for all analyses conducted with the most complete matrix (90% of occupancy), being at odds not only with the sparser but more gene-rich supermatrices (75% and 50% supermatrices) or with the matrices optimizing phylogenegic informativeness and the most conserved genes, but also with previous hypotheses based on morphology, development or other molecular data sets. We discuss the implications of these findings in the context of the ever more prevalent quest for completeness in phylogenomic studies.

Phylogenetic relationships of the subfamily Pyrgulinae (Gastropoda: Caenogastropoda: Hydrobiidae) with emphasis on the genus Dianella Gude, 1913

Zootaxa ◽  
2005 ◽  
Vol 891 (1) ◽  
pp. 1 ◽  
Author(s):  
Magdalena Szarowska ◽  
Andrzej Falniowski ◽  
FRANK Riedel ◽  
Thomas Wilke
Keyword(s):  
Type Species ◽  
Sister Group ◽  
Molecular Data ◽  
Character Evolution ◽  
Phylogenetic Position ◽  
Sister Group Relationship ◽  
Data Sets ◽  
Sequencing Data ◽  
The Family ◽  
Anatomical Characters

The phylogenetic position of the subfamily Pyrgulinae within the superfamily Rissooidea has been discussed very controversially. Different data sets not only led to different evolutionary scenarios but also to different systematic classifications of the taxon. The present study uses detailed anatomical data for two pyrgulinid taxa, the type species of the subfamily, Pyrgula annulata (Linnaeus, 1767), and the type species of the little known genus Dianella, D. thiesseana (Kobelt, 1878), as well as DNA sequencing data of three gene fragments from representatives of eight rissooidean families to A) infer the phylogenetic position of Pyrgulinae with emphasis on its relationships within the family Hydrobiidae, B) to study the degree of concordance between anatomyand DNAbased phylogenies and C) to trace the evolution of anatomical characters along a multi-gene molecular phylogeny to find the anatomical characters that might be informative for future cladistic analyses. Both anatomical and molecular data sets indicate either a very close or even sister-group relationship of Pyrgulinae and Hydrobiinae. However, there are major conflicts between the two data sets on and above the family level. Notably, Hydrobiidae is not monophyletic in the anatomical analysis. The reconstruction of anatomical character evolution indicates that many of the characters on which the European hydrobioid taxonomy is primarily based upon are problematic. The inability to clearly separate some hydrobiids from other distinct families based on those characters might explain why until only a few years ago, "Hydrobiidae" was a collecting box for numerous rissooidean taxa (mostly species with shells small and lacking any characteristic features). The present study not only stresses the need for comprehensive molecular studies of rissooidean taxa, it also demonstrates that much of the problems surrounding anatomical analyses in rissooidean taxa are due to the lack of comprehensive data for many representatives. In order to aid future comparativeanatomical studies and a better understanding of character evolution in the species-rich family Hydrobiidae, detailed anatomical descriptions for P. annulata and D. thiesseana are provided.Key words: Pyrgulinae, Pyrgula, Dianella, Hydrobiidae, phylogeny, DNA, anatomy, Greece

scholarly journals Cretaceous origin and repeated tertiary diversification of the redefined butterflies

2011 ◽  
Vol 279 (1731) ◽  
pp. 1093-1099 ◽  
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.

Cladistic relationships among higher groups of Heteroptera: congruence between morphological and molecular data sets

1993 ◽  
Vol 24 (2) ◽  
pp. 121-137 ◽  
Author(s):  
Ward C. Wheeler ◽  
Ranhy Bang ◽  
Randall T. Schuh
Keyword(s):  
Sister Group ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Sister Group Relationship ◽  
Molecular Evidence ◽  
Data Sets ◽  
Nuclear Rdna ◽  
History Of ◽  
Morphological And Molecular Data

AbstractThe monophyly of the 7 infraorders of Heteroptera and history of higher group concepts and interrelationships within the Heteroptera are briefly reviewed. Data from 31 morphological characters are combined with 669 bases of 18S nuclear rDNA for 29 taxa, including several outgroups to the Heteroptera, to produce a phylogeny based on the total available evidence. The molecular data alone and in conjunction with morphological data indicate that: the Homoptera are probably not monophyletic; the Auchenorrhyncha are the sister group of Coleorrhyncha + Heteroptera ; the Enicocephalomorpha are the sister group of remaining Heteroptera; the Dipsocoromorpha are the sister group of remaining Heteroptera; the Gerromorpha are the sister group of remaining Heteroptera; the Nepomorpha are the sister group of remaining Heteroptera; the Leptopodomorpha are the sister group of the Cimicomorpha + Pentatomomorpha. The molecular evidence corroborates the morphologically based theory of a sister group relationship between Aradoidea and trichophoran Pentatomomorpha. This scheme deviates from that previously published by Schuh, in which the Leptopodomorpha were treated as the sister group of the Nepomorpha.

scholarly journals Phylogenetic position and taxonomy of Cycloseris explanulata and C. wellsi (Scleractinia: Fungiidae): lost mushroom corals find their way home

2012 ◽  
Vol 81 (3) ◽  
pp. 125-146 ◽  
Author(s):  
Francesca Benzoni ◽  
Roberto Arrigoni ◽  
Fabrizio Stefani ◽  
Bastian T. Reijnen ◽  
Simone Montano ◽  
...  
Keyword(s):  
Molecular Study ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Distribution Data ◽  
Data Sets ◽  
Free Living ◽  
New Findings ◽  
The Family ◽  
Ecological Implications ◽  
History Of

The scleractinian species Psammocora explanulata and Coscinaraea wellsi were originally classified in the family Siderastreidae, but in a recent morpho-molecular study it appeared that they are more closely related to each other and to the Fungiidae than to any siderastreid taxon. A subsequent morpho-molecular study of the Fungiidae provided new insights regarding the phylogenetic relationships within that family. In the present study existing molecular data sets of both families were analyzed jointly with those of new specimens and sequences of P. explanulata and C. wellsi. The results indicate that both species actually belong to the Cycloseris clade within the family Fungiidae. A reappraisal of their morphologic characters based on museum specimens and recently collected material substantiate the molecular results. Consequently, they are renamed Cycloseris explanulata and C. wellsi. They are polystomatous and encrusting like C. mokai, another species recently added to the genus, whereas all Cycloseris species were initially thought to be monostomatous and free-living. In the light of the new findings, the taxonomy and distribution data of C. explanulata and C. wellsi have been updated and revised. Finally, the ecological implications of the evolutionary history of the three encrusting polystomatous Cycloseris species and their free-living monostomatous congeners are discussed.

Phylogeny of Echiura updated, with a revised taxonomy to reflect their placement in Annelida as sister group to Capitellidae

2020 ◽  
Vol 34 (1) ◽  
pp. 101 ◽  
Author(s):  
Ryutaro Goto ◽  
James Monnington ◽  
Marija Sciberras ◽  
Isao Hirabayashi ◽  
Greg W. Rouse
Keyword(s):  
Molecular Phylogeny ◽  
Deep Sea ◽  
Sister Group ◽  
Molecular Data ◽  
Monterey Bay ◽  
Phylogenetic Studies ◽  
Littoral Zones ◽  
Family Level ◽  
Relationship Of ◽  
The Relationship

Echiura (commonly called spoon worms) are derived annelids that have an unsegmented sausage-shaped body with a highly extensible anterior end (i.e. a proboscis). Echiura currently contains two superfamilies: Echiurioidea (with Echiuridae, Urechidae and Thalassematidae) and Bonellioidea (with Bonelliidae, and Ikedidae). Ikedidae contains only Ikeda, which is distinctive in having a huge trunk, a highly elongate proboscis with stripes or dots, and numerous gonoducts. A recent molecular phylogeny of Echiura recovered Ikedidae as the sister group to Bonelliidae. However, due to relatively low support values for the monophyly of Bonelliidae, this relationship remains problematic. In this study, we reinvestigated the relationship of Bonelliidae and Ikedidae using an expanded dataset with more taxa and genes. In contrast to the previous results, our analyses strongly support that Ikeda is nested within Bonelliidae due to the placement of Maxmuelleria. On the basis of this result, we synonymise Ikedidae with Bonelliidae and transfer Ikeda to the latter, the diagnosis of which is amended. In addition, we synonymise Urechidae with its sister group Echiuridae because they share the synapomorphy of having anal chaetae rings. Furthermore, considering that recent phylogenetic studies have consistently recovered Echiura as the sister group to Capitelliidae within Annelida, we drop the rank of the echiuran clade to family-level and propose a revised classification: Thalassematidae with two subfamilies, Thalassematinae (with two tribes Echiurini and Thalassematini) and Bonelliinae. In addition, we identified a sample collected from the deep sea (~1820 m) of Monterey Bay, California, based on its molecular data. This terminal unexpectedly formed the sister group to the eight genera of Thalassematini, most members of which are inhabitants of littoral zones.

Back to the Future? Molecules Take Us Back to the 1925 Classification of the Lembophyllaceae (Bryopsida)

2009 ◽  
Vol 34 (3) ◽  
pp. 443-454 ◽  
Author(s):  
Dietmar Quandt ◽  
Sanna Huttunen ◽  
Ray Tangney ◽  
Michael Stech
Keyword(s):  
Single Species ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
New Family ◽  
Morphological Studies ◽  
The Family ◽  
Family Level ◽  
Plastid Markers ◽  
Pleurocarpous Moss

Although the Lembophyllaceae has undergone considerable revision during the last century, the generic and familial level relationships of this pleurocarpous moss family are still poorly understood. To address this problem, a generic revision of the Lembophyllaceae based on molecular data was undertaken. We analyzed two plastid markers, the trnL-trnF and the psbT-psbH region in combination with the ITS2 of nuclear ribosomal DNA. The molecular data reveal that the current circumscription of the family is too narrow and that several genera previously placed in the Lembophyllaceae should be reincluded. The family includes: Bestia, Camptochaete, Dolichomitra, Dolichomitriopsis, Fallaciella, Fifea, Isothecium, Lembophyllum, Looseria stat. nov., Pilotrichella, Rigodium, Tripterocladium, and Weymouthia. Looseria contains a single species: Looseria orbiculata comb. nov. Acrocladium is excluded and provisionally accommodated in the Lepyrodontaceae. Generic limits supported by the molecular data support a return to the early twentieth century family concept of Brotherus. The analyses indicate that the segregate genus Orthostichella is distinct from its parent genus Pilotrichella, probably at the family level. Whereas Pilotrichella is resolved within the Lembophyllaceae, Orthostichella clusters with Porotrichum and Porothamnium forming a clade (OPP-clade) sister to the remaining Neckeraceae and Lembophyllaceae. Hence, the Neckeraceae is paraphyletic. Recognition of the OPP-clade as a new family is desirable but awaits the results of detailed ongoing morphological studies.

scholarly journals Polyphyly and homoplasic structures in rhizosolenioid diatom genera: a review

2019 ◽  
Vol 152 (2) ◽  
pp. 142-149
Author(s):  
Richard W. Jordan ◽  
Matt P. Ashworth ◽  
Yuki Uezato ◽  
Schonna R. Manning
Keyword(s):  
Electron Microscope ◽  
Literature Review ◽  
Scanning Electron Microscope ◽  
Strong Support ◽  
Molecular Data ◽  
Literature Survey ◽  
Single Family ◽  
The Family ◽  
Family Level ◽  
Scanning Electron

Background and aims – Traditionally, extant rhizosolenioid diatom genera have been placed in a single family, the Rhizosoleniaceae. However, preliminary molecular data suggested that the family might be polyphyletic. Therefore, a literature review of the morphological, ultrastructural and molecular data of the rhizosolenioid genera was undertaken. Methods – In addition to the literature survey, the location of the rimoportula in a number of rhizosolenioid genera was investigated by breaking the valves and observing the fragments in the scanning electron microscope. Key results – The data provides strong support for the previous separation of Proboscia and Rhizosolenia at the family level (Probosciaceae vs. Rhizosoleniaceae), with the rimoportula being located at the tip of the proboscis in Proboscia, or with an internal labia at the base of the hollow tubular rimoportula (= spine or process) in Rhizosolenia and Pseudosolenia. Conclusions – The data suggests that a number of rhizosolenioid genera should be transferred to other families, and that gene sequences of two genera (Dactyliosolen and Neocalyptrella) are needed as their morphological features differ markedly from those of the Rhizosoleniceae s. str. (Rhizosolenia, Guinardia, Pseudosolenia).

scholarly journals An Analysis of the Street Tree Population of Greater Melbourne at the Beginning of the 21st Century

2006 ◽  
Vol 32 (4) ◽  
pp. 155-163
Author(s):  
Stephen Frank ◽  
Glenn Waters ◽  
Russell Beer ◽  
Peter May
Keyword(s):  
Data Sets ◽  
Botanical Composition ◽  
Future Studies ◽  
Prunus Cerasifera ◽  
Tree Population ◽  
Tree Inventory ◽  
Street Tree ◽  
The Family ◽  
Family Level ◽  
Prunus Spp

An audit of the street tree population of Melbourne, Victoria, Australia, was undertaken to establish its size and botanical composition as a reference point for future studies. The 31 independent municipalities that comprise metropolitan Melbourne were approached to provide information on their respective street tree populations. Where available, data from individual municipalities on population, area, and total street length were also collected. Of the 31 municipalities surveyed, 23 had undertaken some form of street tree inventory or audit. These individual data sets were combined into a single database. Data queries were then undertaken to obtain a range of information. A total of 922,353 trees, comprising 1127 taxa, were captured in this superset of data. Australian native plants made up the majority of the trees with 60% of the total. Of the Australian native taxa, wattles (Acacia spp.), gums or eucalypts (Eucalyptus spp.), paperbarks (Melaleuca spp.), bottlebrush (Callistemon spp.), and Queensland brush box (Lophostemon confertus [R. Br.] Peter G. Wilson and Waterhouse) comprised 394,730 individuals (43% of all trees). Of the exotic taxa, Prunus spp. were the most common with 86,227 individuals (9% of the total). Queensland brush box was the most common taxon surveyed with 61,959 individuals. Purple-leaf cherry plum (Prunus cerasifera Ehrh. ‘Nigra’) was the most common exotic taxon with 35,402 individuals. An analysis of the diversity of this population showed that it meets a set of minimum diversity criteria apart from the dominance of the Myrtaceae at the family level.

Early embryology of Vochysiaceae and some insights into its phylogeny and intrafamilial taxonomy

Phytotaxa ◽  
2020 ◽  
Vol 443 (3) ◽  
pp. 211-257
Author(s):  
RENATA CARMO-OLIVEIRA ◽  
LUCIANA NASCIMENTO CUSTÓDIO ◽  
BERTA LANGE DE MORRETES ◽  
PAULO EUGÊNIO OLIVEIRA
Keyword(s):  
Developmental Stages ◽  
Embryo Sac ◽  
Sister Group ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Its Phylogeny ◽  
The Family

Embryological data provides insights into the taxonomy and evolution of angiosperms.  Vochysiaceae is a mostly Neotropical family whose phylogenetic position was greatly influenced by reconstructions based on molecular data, and despite its monosymmetric and oligostemonous flowers, was included as a sister group of polysymmetric and polystemonous Myrtaceae. However, molecular data has yet to resolve the relationships between the genera inside the family. We analysed the early embryology of some species of five out of the six generally accepted Neotropical genera using sequential histological analyses to compare the microsporogenesis and gametogenesis and megasporogenesis and gametogenesis between clades and with the embryology of the well-studied Myrtales. We observed some marked differences in timing and developmental stages, which somewhat corroborate the clades defined from molecular data. Multiple archesporium and embryo sacs, as well as megagametophyte maturation and fertilization long after anthesis, characterized the Qualea-Ruizteranea-Callisthene (QRC) clade, while single embryo sac mature at anthesis characterized the Vochysia-Salvertia (VS) clade. Tri-cellular pollen only occurred in Salvertia convallariodora. Seven of the eight main embryological features supported the Myrtales as present in Vochysiaceae and the remaining one, inner integument with two layers of cells, was observed in some Qualea. Thus, the studied Vochysiaceae embryology conforms very well within the order and only their strongly monosymmetric and oligostemonous flowers are less common among Myrtales.

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