trnL-F and rpl16 Sequence Data and Dense Taxon Sampling Reveal Monophyly of Unilocular Anthered Gomphrenoideae (Amaranthaceae) and an Improved Picture of Their Internal Relationships

2009 ◽  
Vol 34 (1) ◽  
pp. 57-67 ◽  
Author(s):  
Ivonne Sánchez del-Pino ◽  
Thomas Borsch ◽  
Timothy J. Motley
Keyword(s):  
Pollen Morphology ◽  
New World ◽  
Sequence Data ◽  
Taxon Sampling ◽  
Bayesian Analyses ◽  
Phylogenetic Studies ◽  
The Family ◽  
Large Genus ◽  
Internal Relationships ◽  
Generic Relationships

The Amaranthaceae-Chenopodiaceae alliance has been the focus of several phylogenetic studies, but major questions concerning the internal relationships of Amaranthaceae still remain unanswered. This study aims to test the monophyly of the subfamily Gomphrenoideae and to examine the generic relationships within this group. Parsimony and Bayesian analyses of trnL-F and rpl16 show that the subfamily Gomphrenoideae is monophyletic. The clade of Gomphrenoideae represents a large and diverse radiation of the Amaranthaceae in the New World. Unilocular anthers are a morphological synapomorphy for Gomphrenoideae that was derived from bilocular anthers. Three major clades are resolved: the Gomphrenoids, the Alternantheroids, and the Iresinoids, which are largely supported by pollen morphology. The Iresinoid clade is sister to Alternantheroids plus Gomphrenoids, rendering metareticulate pollen as the synapomorphy for the latter two clades. Tribes and subtribes delimited by androecium and inflorescence characters are poly- or paraphyletic. Several genera are monophyletic including the large genus Alternanthera, whereas Gomphrena is polyphyletic. Irenella and Woehleria are resolved within Iresine whereas Blutaparon and Lithophila fall within the polyphyletic Gomphrena. The trnL-F and rpl16 sequence data are the most variable chloroplast regions examined to date for the family and are highly effective in resolving relationships in Amaranthaceae.

Phylogenetic relationships of Mediterranean black corals (Cnidaria : Anthozoa : Hexacorallia) and implications for classification within the order Antipatharia

2018 ◽  
Vol 32 (5) ◽  
pp. 1102 ◽  
Author(s):  
M. Bo ◽  
M. Barucca ◽  
M. A. Biscotti ◽  
M. R. Brugler ◽  
A. Canapa ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Data ◽  
Coral Fauna ◽  
Black Coral ◽  
Phylogenetic Studies ◽  
Black Corals ◽  
The Family ◽  
The Mediterranean ◽  
Its1 And Its2 Rdna ◽  
Its1 And Its2

The Mediterranean black coral fauna includes type species of four antipatharian genera belonging to four different families, therefore phylogenetic studies hold great potential for enhancing systematics within the order. The analysis of six Mediterranean antipatharian species by means of nuclear sequence data of internal transcribed spacer (ITS1 and ITS2) rDNA confirms the separation into different families, as was previously noted on a morphological basis, with a clear distinction of the family Leiopathidae, whose position is supported by a unique number of mesenteries and lack of spines on thicker ramifications. The position of a newly recorded black coral species for the Mediterranean basin belonging to the genus Phanopathes is discussed. Antipathes dichotoma, the type species of the genus Antipathes, on which the order Antipatharia was based, does not group with other members of the family Antipathidae. Supporting a recent finding based on mitochondrial markers, this suggests a critical need for revision of the families that will be impacted by reassignment of this nomenclaturally important taxon.

scholarly journals Rhapsody in emerald: phylogenetic framework for Lestidae with reference to the systematic position of Chalcolestes Kennedy

2022 ◽  
Vol 25 ◽  
pp. 16-21
Author(s):  
Thomas J. Simonsen ◽  
Marcus Glahder ◽  
Thomas Pape ◽  
Kent Olsen ◽  
Marie Djernæs
Keyword(s):  
New World ◽  
Sequence Data ◽  
Strong Support ◽  
Systematic Position ◽  
The Other ◽  
Valid Genus ◽  
The Family ◽  
Statistical Support ◽  
Phylogenetic Framework ◽  
Molecular Dataset

We reconstruct a phylogenetic framework for the zygopteran family Lestidae based on a molecular dataset comprised of sequence data from the genes COI, 16S, 18S, 28S, and ITS1+2 from 41 ingroup taxa and 8 outgroup taxa with emphasis on the systematic position of the genus Chalcolestes Kennedy. We recover Lestidae as monophyletic with good statistical support. The family falls into two subequal clades. One, comprising the genus Sympecma Burmeister and Lestes Leach sensu lato (including the genus Archi­lestes Selys) is poorly to moderately supported. While the other, comprising the genera Austrolestes Tillyard, Indolestes Fraser, Orolestes McLachlan, and Chalcolestes is strongly supported. Chalcolestes is recovered as sister to the Oriental genus Orolestes with strong support. Our results thus support that Chalcolestes is a valid genus not closely related to Lestes. Monophyly of Lestes requires inclusion of the New World genus Archilestes, and our results support the need for a thorough revision of Lestes.

Transfer of four species of Cryptantha to the genus Johnstonella (Boraginaceae)

Phytotaxa ◽  
2019 ◽  
Vol 425 (5) ◽  
pp. 279-289
Author(s):  
MICHAEL G. SIMPSON ◽  
MAKENZIE E. MABRY ◽  
KRISTEN HASENSTAB-LEHMAN
Keyword(s):  
Sequence Data ◽  
Strong Support ◽  
Herbaceous Plant ◽  
New Combinations ◽  
Morphological Similarity ◽  
Additional Species ◽  
Phylogenetic Studies ◽  
The Family ◽  
Molecular Phylogenetic ◽  
Close Relatives

Based on a previous molecular phylogenetic analysis, Cryptantha, an herbaceous plant genus of the family Boraginaceae, subtribe Amsinckiinae, was split into five genera: Eremocarya, Greeneocharis, Johnstonella, Oreocarya, and a reduced Cryptantha, the last in two separate clades. As a result of this study, Johnstonella was expanded to 13 species and 15 minimum-rank taxa, these formerly classified in Cryptantha s.l. More recent analyses of this complex, with an increased sample size and high-throughput sequence data, indicate that four additional Cryptantha species not previously sampled—C. albida, C. mexicana, C. texana—plus what was originally identified as C. hispida nest within Johnstonella with strong support. However, the identity of C. hispida used in this analysis is now in doubt. The material used likely represents a new species, in the process of being investigated. Two additional species not sequenced to date—C. geohintonii and C. gypsites—are clearly close relatives of C. albida and C. mexicana, based on morphological similarity. In order to maintain monophyly of genera, we here make new combinations in transferring four of these species from Cryptantha to Johnstonella, with the new combinations Johnstonella albida, J. geohintonii, J. gypsites, and J. mexicana. We delay the transfer of Cryptantha texana to Johnstonella because of its morphological similarity to other species that clearly nest within Cryptantha s.s. These same molecular phylogenetic studies may also support the transfer of two previously recognized Johnstonella species—J. echinosepala and J. micromeres—to Cryptantha, one to each of two separate clades. Additional phylogenetic studies focusing on some of these taxa are needed to confirm the position of these latter three species and the possible recognition of a new genus in the complex.

Studies on Parmulariaceae I. A phylogeny based on available sequence data; introducing Parmulariales ord. nov., and Hemigraphaceae, Melaspileellaceae and Stictographaceae fam. nov.

Phytotaxa ◽  
2018 ◽  
Vol 369 (2) ◽  
pp. 63 ◽  
Author(s):  
DONG-QIN DAI ◽  
LI-ZHOU TANG ◽  
CHAO LIU ◽  
HAI-BO WANG ◽  
KEVIN D. HYDE
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Tree ◽  
Type Species ◽  
Sequence Data ◽  
Sensu Stricto ◽  
New Order ◽  
Bayesian Analyses ◽  
Phylogenic Analysis ◽  
The Family

The family Parmulariaceae comprises three polyphyletic genera, but with very little data in GenBank and is presently placed in the order Asterinales. In this study, we re-analyze the available sequence data for taxa of the family and re-examine the type species of Hemigrapha, Inocyclus and Parmularia. The phylogenetic tree generated from maximum likelihood and Bayesian analyses of combined LSU-SSU sequence data demonstrate the relationships among Hemigrapha, Inocyclus and Parmularia species, and the relations of Buelliella, Karschia, Labrocarpon, Lembosia, Melaspileella, Melaspileopsis and Stictographa. We introduce Parmulariales ord. nov. to accommodate Parmulariaceae and the order Asterinales accommodates Asterinaceae, Asterotexaceae, Hemigraphaceae fam. nov., Melaspileellaceae fam. nov. and Stictographaceae fam. nov. Notes for each new order and families are provided. We confirm that Asterinaceae sensu lato is distant from Asterinaceae sensu stricto in the phylogenic analysis. The classification presented here is provisional, as more species are needed to re-collected and sequenced. We expect further support for our ordinal and familial lineages, as well as further novel lineages.

scholarly journals Diversification of New Zealand weta (Orthoptera: Ensifera: Anostostomatidae) and their relationships in Australasia

2008 ◽  
Vol 363 (1508) ◽  
pp. 3427-3437 ◽  
Author(s):  
Renae C Pratt ◽  
Mary Morgan-Richards ◽  
Steve A Trewick
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
New Zealand ◽  
New Caledonia ◽  
Sequence Data ◽  
Species Level ◽  
Molecular Dating ◽  
Bayesian Analyses ◽  
Dna Sequence Data ◽  
The Family

New Zealand taxa from the Orthopteran family Anostostomatidae have been shown to consist of three broad groups, Hemiandrus (ground weta), Anisoura/Motuweta (tusked weta) and Hemideina – Deinacrida (tree–giant weta). The family is also present in Australia and New Caledonia, the nearest large land masses to New Zealand. All genera are endemic to their respective countries except Hemiandrus that occurs in New Zealand and Australia. We used nuclear and mitochondrial DNA sequence data to study within genera and among species-level genetic diversity within New Zealand and to examine phylogenetic relationships of taxa in Australasia. We found the Anostostomatidae to be monophyletic within Ensifera, and justifiably distinguished from the Stenopelmatidae among which they were formerly placed. However, the New Zealand Anostostomatidae are not monophyletic with respect to Australian and New Caledonian species in our analyses. Two of the New Zealand groups have closer allies in Australia and one in New Caledonia. We carried out maximum-likelihood and Bayesian analyses to reveal several well supported subgroupings. Our analysis included the most extensive sampling to date of Hemiandrus species and indicate that Australian and New Zealand Hemiandrus are not monophyletic. We used molecular dating approaches to test the plausibility of alternative biogeographic hypotheses for the origin of the New Zealand anostostomatid fauna and found support for divergence of the main clades at, or shortly after, Gondwanan break-up, and dispersal across the Tasman much more recently.

On the phylogenetic relationships of hadromerid and poecilosclerid sponges

2007 ◽  
Vol 87 (6) ◽  
pp. 1585-1598 ◽  
Author(s):  
Kord M. Kober ◽  
Scott A. Nichols
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Full Length ◽  
Taxon Sampling ◽  
Short Segment ◽  
Data Support ◽  
The Family ◽  
Clade C ◽  
Internal Relationships

Recent phylogenetic analyses of demosponges have suggested that the order Poecilosclerida is monophyletic and nested within the paraphyletic ‘order’ Hadromerida. Until now, this result has rested upon very limited taxon sampling of SSU sequences and partial LSU sequences. We collected and analysed additional full-length SSU and LSU sequences to test the validity and position of the poecilosclerid/hadromerid clade within demosponges, and we sampled a short segment of the LSU from diverse hadromerids to explore the internal relationships of Hadromerida. Our data strongly support the existence of a hadromerid/poecilosclerid clade that is sister to a poorly characterized group of halichondrid and agelasid species (‘Clade C’). We find support for the monophyly of the hadromerid families Polymastiidae, Placospongiidae and Timeidae, and conditional support for the family Suberitidae. Furthermore, both LSU and SSU data support a clade that includes a mixture of species assigned to the families Tethyidae and Hemiasterellidae (TETH/HEM) and a mixed clade including members of the families Clionaidae and Spirastrellidae (CLIO/SPIR). The family Placospongiidae is reconstructed as sister to the clade CLIO/SPIR and the family Timeidae is supported as sister to the clade TETH/HEM. The order Poecilosclerida is most closely allied with the Placospongiidae/CLIO/SPIR clade.

scholarly journals What isAtraphaxisL. (Polygonaceae, Polygoneae): cryptic taxa and resolved taxonomic complexity instead of the formal lumping and the lack of morphological synapomorphies

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1977 ◽  
Author(s):  
Olga V. Yurtseva ◽  
Oxana I. Kuznetsova ◽  
Maria E. Mavrodieva ◽  
Evgeny V. Mavrodiev
Keyword(s):  
Life History ◽  
Pollen Morphology ◽  
Plastid Genome ◽  
Sequence Data ◽  
Morphological Data ◽  
Bayesian Analyses ◽  
Dna Sequence Data ◽  
Phylogenetic Reconstructions ◽  
Generic Composition ◽  
Cryptic Taxa

Backgrounds:The recently proposed recircumscription of the genusAtraphaxis(incl.AtraphaxissectionOvczinnikoviaO.V. Yurtseva ex. S. Tavakkoli andPolygonumsect.SpinescentiaBoissier (=A.sect.PolygonoidesS. Tavakkoli, Kaz. Osaloo & Mozaff.) makes this genus fairly heterogeneous and therefore almost undefinable based on morphology. The critical comprehensive reappraisal of the group is necessary.Methods:Using the DNA sequence data (ITS1&2 regions of nrDNA and combinedtrnL intron +trnL–F IGS and rpl32–trnL(UAG)IGS regions of plastid genome), Maximum Likelihood (ML) and Bayesian analyses (BI) were applied for phylogenetic reconstructions of the tribe Polygoneae with special attention toAtraphaxis, and related taxa. Maximum parsimony reconstructions of the evolution of perianth morphology and sporoderm ornamentation in the tribe Polygoneae were also performed. Life history, morphology of shoots, leaf blades, ocreas, perianth and achene morphology, ultrasculpture of achene surface, and pollen morphology were compared, and SEM and LM images were provided.Principal findings:The generaAtraphaxisandPolygonumwere found to be widely polyphyletic. The rarest and morphologically remarkable endemic of Tian-Shan and PamirAtraphaxis ovczinnikovii(Atraphaxissect.OvczinnikoviaO.V. Yurtseva ex. S. Tavakkoli) was confirmed to be a sister of the clade (Atraphaxis+Polygonumsect.Spinescentia) in plastid topology. The genusBactria (=Atraphaxissect.Ovczinnikovia), which circumscribes two species, is newly established as a result of this analyses. Morphological data confirm the originality of the taxon.Discussion:We are arguing for a narrow delimitation ofAtraphaxiswith petalloid segments and striato-perforate sporoderm ornamentation as morphological synapomorphies. The recently proposed inclusion ofPolygonumsect.SpinescentiainAtraphaxisis fairly questionable from a morphological standpoint. The rank ofPolygonumsect.Spinescentiarequires further clarification. The generic composition of the tribe Polygoneae also requires future reappraisals.

scholarly journals Molecular phylogeny, morphology and their implications for the taxonomy of Eriocaulaceae

Rodriguésia ◽  
2012 ◽  
Vol 63 (1) ◽  
pp. 001-019 ◽  
Author(s):  
Ana M. Giulietti ◽  
Maria José G. Andrade ◽  
Vera L. Scatena ◽  
Marcelo Trovó ◽  
Alessandra I. Coan ◽  
...  
Keyword(s):  
Population Genetics ◽  
Bayesian Inference ◽  
Molecular Phylogeny ◽  
New World ◽  
Additional Data ◽  
Phylogenetic Studies ◽  
The Family ◽  
Molecular Phylogenetic ◽  
Taxonomic Changes ◽  
Anatomical Characters

The pantropical family Eriocaulaceae includes ten genera and c. 1,400 species, with diversity concentrated in the New World. The last complete revision of the family was published more than 100 years ago, and until recently the generic and infrageneric relationships were poorly resolved. However, a multi-disciplinary approach over the last 30 years, using morphological and anatomical characters, has been supplemented with additional data from palynology, chemistry, embryology, population genetics, cytology and, more recently, molecular phylogenetic studies. This led to a reassessment of phylogenetic relationships within the family. In this paper we present new data for the ITS and trnL-F regions, analysed separately and in combination, using maximum parsimony and Bayesian inference. The data confirm previous results, and show that many characters traditionally used for differentiating and circumscribing the genera within the family are homoplasious. A new generic key with characters from various sources and reflecting the current taxonomic changes is presented.

Position of Moina wierzejskii Richard, 1895 (Crustacea: Cladocera) within the genus Moina Baird, 1850 in the light of new morphological data

Zootaxa ◽  
2020 ◽  
Vol 4820 (3) ◽  
pp. 506-522
Author(s):  
ANNA N. NERETINA ◽  
ANNA G. KIRDYASHEVA ◽  
ALEXEY A. KOTOV
Keyword(s):  
New World ◽  
Resting Eggs ◽  
Morphological Data ◽  
Undescribed Species ◽  
European Species ◽  
Phylogenetic Studies ◽  
Thoracic Limb ◽  
The Family ◽  
Unusual Combination ◽  
Strong Position

The family Moinidae (Crustacea: Cladocera) is intensively studied recently. Last genetic investigations revealed a huge diversity of species in the genus Moina Baird, 1850, comparable with the number of species in the genus Daphnia O.F. Müller, 1776. However, unlike daphniids, the taxonomy of moinids is understudied. Along with new still undescribed species, there are many inadequately described and illegitimately forgotten taxa within Moinidae. Moinids of tropical and subtropical regions remain especially poorly studied, and their features are ignored in recent intergeneric systems. Here we redescribe the morphology of M. wierzejskii Richard, 1895, a peculiar Moina from the New World, and discuss its position within the genus Moina s.l. In the taxonomic scheme, designed for European moinids, M. wierzejskii takes an intermediate position between subgenera Exomoina Hudec, 2010 and Moina s.str. Similarly to European species belonging to M. (Exomoina), females of M. wierzejskii have a modified Ilyocryptus-like labrum and an ephippium with two resting eggs. However, the males have no exopod on the thoracic limb I which suggests that this species is closer to the subgenus Moina s.str. The lack of exopod on male thoracic limb I was also marked in another species of the genus from the New World, M. hutchinsoni Brehm, 1937. To date such unusual combination of morphological features is unknown for any moinids from the Old World and Australia. We hope that our observations will stimulate deep phylogenetic studies of peculiar moinids inhabiting the New World.

A five-marker molecular phylogeny of the Styphelieae (Epacridoideae, Ericaceae) supports a broad concept of Styphelia

2015 ◽  
Vol 28 (6) ◽  
pp. 368 ◽  
Author(s):  
Caroline Puente-Lelièvre ◽  
Michael Hislop ◽  
Mark Harrington ◽  
Elizabeth A. Brown ◽  
Maria Kuzmina ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Morphological Diversity ◽  
Morphological Characters ◽  
Bayesian Analyses ◽  
Close Phylogenetic Relationship ◽  
Broad Concept ◽  
Molecular Phylogenetic ◽  
Large Genus ◽  
Plastid Markers

The Styphelieae is the largest of the seven tribes within the subfamily Epacridoideae Arn. (Ericaceae Juss.). Recent molecular phylogenetic work has resulted in the recircumscription of some genera and the erection of new ones, but several non-monophyletic genera remain. Most of them are concentrated in the well-supported Styphelia–Astroloma clade, which contains species currently assigned to Leucopogon R.Br., Styphelia Sm., Astroloma R.Br., Croninia J.M. Powell and Coleanthera Stschegl. Parsimony and Bayesian analyses of sequence data from four plastid markers (rbcL, matK, trnH–psbA, and atpB–rbcL), and the nuclear ribosomal internal transcribed spacer (ITS) for 207 taxa corroborate the polyphyly of the genera Astroloma, Leucopogon and Styphelia and resolve 12 well supported groups. Of these groups, two can be distinguished by unique morphological features and another six by different character combinations. The remaining groups are morphologically heterogeneous and inconsistent, and not readily distinguishable. A number of species remain ungrouped either because their phylogenetic relationships are not clear or because they do not show strong morphological affinities with the group to which they have a close phylogenetic relationship. Translating the results into a phylogenetic classification is a choice between accepting a single, large genus or at least 12 smaller genera. The first option would result in a heterogeneous assemblage conveying limited morphological information. The multi-generic option would be a better reflection of the morphological diversity of the clade, but would result in many genera lacking readily observable, diagnostic morphological characters. We prioritise the nomenclatural stability inherent in the former approach and advocate expanding Styphelia to include all taxa in the Styphelia–Astroloma clade.

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