scholarly journals Genus-level phylogeny of cephalopods using molecular markers: current status and problematic areas

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4331 ◽  
Author(s):  
Gustavo Sanchez ◽  
Davin H.E. Setiamarga ◽  
Surangkana Tuanapaya ◽  
Kittichai Tongtherm ◽  
Inger E. Winkelmann ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Morphological Characters ◽  
Molecular Dating ◽  
Current Status ◽  
Genus Level ◽  
Extant Species ◽  
The Family ◽  
Open Access Resource ◽  
Near Future ◽  
Access Resource

Comprising more than 800 extant species, the class Cephalopoda (octopuses, squid, cuttlefish, and nautiluses) is a fascinating group of marine conchiferan mollusks. Recently, the first cephalopod genome (of Octopus bimaculoides) was published, providing a genomic framework, which will enable more detailed investigations of cephalopod characteristics, including developmental, morphological, and behavioural traits. Meanwhile, a robust phylogeny of the members of the subclass Coleoidea (octopuses, squid, cuttlefishes) is crucial for comparative and evolutionary studies aiming to investigate the group’s traits and innovations, but such a phylogeny has proven very challenging to obtain. Here, we present the results of phylogenetic inference at the genus level using mitochondrial and nuclear marker sequences available from public databases. Topologies are presented which show support for (1) the monophyly of the two main superorders, Octobrachia and Decabrachia, and (2) some of the interrelationships at the family level. We have mapped morphological characters onto the tree and conducted molecular dating analyses, obtaining congruent results with previous estimates of divergence in major lineages. Our study also identifies unresolved phylogenetic relationships within the cephalopod phylogeny and insufficient taxonomic sampling among squids excluding the Loliginidae in the Decabrachia and within the Order Cirromorphida in the Octobrachia. Genomic and transcriptomic resources should enable resolution of these issues in the relatively near future. We provide our alignment as an open access resource, to allow other researchers to reconstruct phylogenetic trees upon this work in the future.

scholarly journals CHARACTER ASSESSMENT, GENUS LEVEL BOUNDARIES, AND PHYLOGENETIC ANALYSES OF THE FAMILY RHACOPHORIDAE:

2000 ◽  
pp. 1-31 ◽  
Author(s):  
Jeffery A. Wilkinson ◽  
Robert C. Drewes
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Current Status ◽  
Phylogenetic Hypothesis ◽  
Genus Level ◽  
The Family ◽  
Character Assessment

The first comprehensive phylogenetic analysis of the family Rhacophoridae was conducted by Liem (1970) scoring 81 species for 36 morphological characters. Channing (1989), in a reanalysis of Liem’s study, produced a phylogenetic hypothesis different from that of Liem. We compared the two studies and produced a third phylogenetic hypothesis based on the same characters. We also present the synapomorphic characters from Liem that define the major clades and each genus within the family. Finally, we summarize intergeneric relationships within the family as hypothesized by other studies, and the family’s current status as it relates to other ranoid families.

scholarly journals Overview and revision of the extant genera and subgenera of Trogidae (Coleoptera: Scarabaeoidea)

2016 ◽  
Vol 47 (1) ◽  
pp. 53-82 ◽  
Author(s):  
Werner P. Strümpher ◽  
Martin H. Villet ◽  
Catherine L. Sole ◽  
Clarke H. Scholtz
Keyword(s):  
Molecular Phylogeny ◽  
Endemic Species ◽  
Strong Support ◽  
Morphological Characters ◽  
New Combinations ◽  
Genus Level ◽  
Generic Rank ◽  
The Family ◽  
Taxonomic Changes

Extant genera and subgenera of the Trogidae (Coleoptera: Scarabaeoidea) are reviewed. Contemporary classifications of this family have been based exclusively on morphological characters. The first molecular phylogeny for the family recently provided strong support for the relationships between morphologically defined genera and subgenera. On the basis of morphological, molecular and biogeographical evidence, certain taxonomic changes to the genus-level classification of the family are now proposed. The family is confirmed as consisting of two subfamilies, Omorginae Nikolajev and Troginae MacLeay, the former with two genera,OmorgusErichson andPolynoncusBurmeister, and the latter with two genera,TroxFabricius andPhoberusMacLeaystat. rev.Phoberusis restored to generic rank to include all Afrotropical (including Madagascan endemic) species;Afromorgusis confirmed at subgeneric rank within the genusOmorgus; and the monotypic Madagascan genusMadagatroxsyn. n.is synonymised withPhoberus.The current synonymies ofPseudotroxRobinson (withTrox),ChesasBurmeister,LagopelusBurmeister andMegalotroxPreudhomme de Borre (all withOmorgus) are all accepted to avoid creating speculative synonyms before definitive phylogenetic evidence is available. New combinations resulting from restoringPhoberusto a monophyletic genus are listed in Appendix A.

scholarly journals Evolution of seahorses' upright posture was linked to Oligocene expansion of seagrass habitats

2009 ◽  
Vol 5 (4) ◽  
pp. 521-523 ◽  
Author(s):  
Peter R. Teske ◽  
Luciano B. Beheregaray
Keyword(s):  
Fossil Record ◽  
Sequence Data ◽  
Morphological Evolution ◽  
Molecular Techniques ◽  
Molecular Dating ◽  
Upright Posture ◽  
Tectonic Events ◽  
Extant Species ◽  
The Family ◽  
Transitional Forms

Seahorses (Syngnathidae: Hippocampus ) are iconic marine teleosts that are readily identifiable by their upright posture. The fossil record is inadequate to shed light on the evolution of this trait because it lacks transitional forms. There are, however, extant syngnathid species (the pygmy pipehorses) that look like horizontally swimming seahorses and that might represent a surviving evolutionary link between the benthic seahorses and other, free-swimming members of the family Syngnathidae. Using sequence data from five nuclear loci, we confirm the sister taxon relationship between seahorses and pygmy pipehorses. Molecular dating indicates that the two taxa diverged during the Late Oligocene. During this time, tectonic events in the Indo-West Pacific resulted in the formation of vast amounts of new shallow-water areas and associated expansion of seagrass habitats that would have favoured the seahorses’ upright posture by improving their camouflage while not affecting their manoeuvrability negatively. The molecular techniques employed here provide new insights into the evolution of a taxon whose fossil record is incomplete, but whose evolutionary history is so recent that the major stages of morphological evolution are still represented in extant species.

Phylogenetic overview of flat wasps (Hymenoptera, Bethylidae) reveals Elektroepyrinae, a new fossil subfamily

2020 ◽  
Vol 3 (3) ◽  
pp. 269-283
Author(s):  
WESLEY D. COLOMBO ◽  
EVGENY E. PERKOVSKY ◽  
CELSO O. AZEVEDO
Keyword(s):  
Lower Cretaceous ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
New Taxon ◽  
Fossil Species ◽  
Geological Record ◽  
Diverse Families ◽  
The Third ◽  
Extant Species ◽  
The Family

The flat wasps, Bethylidae, are cosmopolitan and one of the most diverse families of Chrysidoidea. Bethylidae have 2,920 described extant species and almost 90 fossil species. The oldest geological record of the family is the Lower Cretaceous, from Lebanese and Spanish ambers and Transbaikalian rock fossils. Here we describe and illustrate one new fossil subfamily of Bethylidae: †Elektroepyrinae subfam. nov. represented by †Elektroepyris Perrichot & Nel from the lowermost Eocene Oise amber (France), which was cladistically assessed against all other eight subfamilies of Bethylidae. The new taxon is easily distinguished from other subfamilies by the forewing venation with the third abscissa of Cu present. Phylogenetic analyses support the monophyly of all subfamilies of Bethylidae, with a matrix with 69 morphological characters and 22 terminal taxa from where †Elektroepyrinae subfam. nov. emerged as independent lineage from all other subfamilies.

scholarly journals A reassessment of the phylogenetic utility of genus-level morphological characters in the family Bogidiellidae (Crustacea, Amphipoda), with description of a new species of Eobogidiella Karaman, 1981

ZooKeys ◽  
2016 ◽  
Vol 610 ◽  
pp. 23-43
Author(s):  
Dmitry A. Sidorov ◽  
Aron D. Katz ◽  
Steven J. Taylor ◽  
Mikhail V. Chertoprud
Keyword(s):  
New Species ◽  
Morphological Characters ◽  
Genus Level ◽  
The Family ◽  
A New Species

PHYLOGENY, BIOGEOGRAPHY AND CHARACTER EVOLUTION OF DORSTENIA (MORACEAE)

2012 ◽  
Vol 69 (3) ◽  
pp. 413-440 ◽  
Author(s):  
T. M. Misiewicz ◽  
N. C. Zerega
Keyword(s):  
Maximum Likelihood ◽  
Life Form ◽  
Sequence Data ◽  
Morphological Characters ◽  
Molecular Dating ◽  
Its Sequence ◽  
The Family ◽  
Storage Organs ◽  
Woody Habit ◽  
Origin Hypothesis

Dorstenia, the second largest genus (105 species) within the Moraceae, is the only genus in the family with woody, herbaceous and succulent species. All but one species of Dorstenia are restricted to the Neotropics or Africa, and it is the only genus in the family with an almost equal transatlantic distribution. This work presents the first molecular phylogeny and the first evolutionary study to examine origin and diversification within the genus. We inferred the phylogeny with ITS sequence data using Bayesian and maximum likelihood approaches. We tracked the evolution of distinct morphological characters and tested for correlated evolution in multiple characters. Time and place of Dorstenia’s origin were estimated to test a post-Gondwanan versus a Gondwanan origin hypothesis using fossil calibrations, Bayesian molecular dating, and maximum likelihood-based ancestral range reconstructions. Our phylogenetic analysis supports the monophyly of Dorstenia; previous subgeneric classifications are polyphyletic and must be re-evaluated. Woody habit, phanerophytic life form, macrospermy, and lack of storage organs are ancestral traits found in African Dorstenia. Evolution of woodiness and macrospermy are correlated. Dorstenia appears to have originated in Africa, radiated into the Neotropics and subsequently re-colonised Africa. Whether or not the extant distribution is the result of vicariance or dispersal is equivocal.

Genus-level revision of the family Phalacridae (Coleoptera: Cucujoidea)

Zootaxa ◽  
2013 ◽  
Vol 3605 (1) ◽  
pp. 1-147 ◽  
Author(s):  
MATTHEW L. GIMMEL
Keyword(s):  
New Species ◽  
Type Species ◽  
Morphological Characters ◽  
Species Group ◽  
Nominal Species ◽  
New Genera ◽  
Genus Level ◽  
The Family ◽  
Tribal Classification ◽  
Phylogenetic Revision

A pre-phylogenetic revision of the family Phalacridae at the genus level is presented. Twenty-eight new generic synonymies are established as follows: Acylomus Sharp 1888 (=Liophalacrus Sharp 1888, syn. nov.; Ganyrus Guillebeau 1894, syn. nov.; Podocesus Guillebeau 1894, syn. nov.; Tinodemus Guillebeau 1894, syn. nov.; Ledorus Guillebeau 1895, syn. nov.; Astenulus Guillebeau 1896, syn. nov.; Afronyrus Švec 2006, syn. nov.), Apallodes Reitter 1873 (=Litolibrus Sharp 1889, syn. nov.; Sphaeropsis Guillebeau 1893, syn. nov.; Gyromorphus Guillebeau 1894, syn. nov.), Augasmus Motschulsky 1858 (=Megischius Guillebeau 1896, syn. nov.; Nematolibrus Sahlberg 1913, syn. nov.), Entomocnemus Guillebeau 1894 (=Stilbomimus Champion 1924, syn. nov.), Grouvelleus Guillebeau 1892 (=Ochrolitoides Champion 1924, syn. nov.; Litotarsus Champion 1925, syn. nov.), Litochrus Erichson 1845 (=Merobrachys Guillebeau 1895, syn. nov.), Litostilbus Guillebeau 1894 (=Pseudolitochrus Liubarsky 1993, syn. nov.), Ochrolitus Sharp 1889 (=Gorginus Guillebeau 1894, syn. nov.), Olibroporus Casey 1890 (=Parasemus Guillebeau 1894, syn. nov.), Olibrosoma Tournier 1889 (=Lichrotus Lyubarsky 1993, syn. nov.), Phaenocephalus Wollaston 1873 (=Phalacratomus Scott 1922, syn. nov.; Heterostilbus Champion 1924, syn. nov.), Phalacrinus Blackburn 1891 (=Sphaerostilbus Champion 1924, syn. nov.), Pseudolibrus Flach 1889 (=Biophytus Guillebeau 1894, syn. nov.; Polyaloxus Guillebeau 1894, syn. nov.), Pycinus Guillebeau 1893 (=Ochrodemus Guillebeau 1893, syn. nov.; Radinus Guillebeau 1893, syn. nov.; Euphalacrus Champion 1925, syn. nov.). Ten new genera and seven new species are described: Antennogasmus, gen. nov. (type species: A. cordatus, sp. nov.), Austroporus, gen. nov. (type species: A. victoriensis (Blackburn)), Malagasmus Gimmel, gen. nov. (type species: M. thalesi, sp. nov.), Malagophytus, gen. nov. (type species: M. steineri, sp. nov.), Neolitochrus, gen. nov. (type species: N. pulchellus (LeConte)), Paracylomus, gen. nov. (type species: P. asiaticus (Champion)), Platyphalacrus, gen. nov. (type species: P. lawrencei, sp. nov.), Ranomafanacrinus, gen. nov. (type species: R. nigrinus, sp. nov.), Steinerlitrus, gen. nov. (type species: S. warreni, sp. nov.), Sveculus, gen. nov. (type species: S. lewisi, sp. nov.). Generic reassignments resulted in 194 new combinations. Nine new names have been established for junior primary and secondary homonyms: Acylomus bicoloratus nom. nov. for Tinodemus bicolor Švec 2002; Acylomus lyubarskyi nom. nov. for Olibrus capriviensis Lyubarsky 1998; Acylomus sveci nom. nov. for Tinodemus reticulatus Švec 2002; Acylomus orientalis nom. nov. for Stilbus similis Švec 1992; Acylomus zdeneki nom. nov. for Afronyrus snizeki Švec 2006; Apallodes championi nom. nov. for Litolibrus ocellatus Champion 1925; Olibrus peringueyi nom. nov. for Olibrus consanguineus Péringuey 1892; Augasmus exquisitus nom. nov. for Litochrus pulchellus Blackburn 1895; Litochrus pronotalis nom. nov. for Augasmus bimaculatus Lyubarsky 1996. A type species is designated for Phalacrinus Blackburn 1891 (P. australis Blackburn 1891). Six new species-group synonymies are established: Acylomus ergoti Casey 1890 (=Tinodemus grouvellei Guillebeau 1894, syn. nov.), Acylomus curvolineatus (Champion 1924) (=Tinodemus meridianus (Švec 1992), syn. nov.; Olibrus stuporatus Lyubarsky 1994, syn. nov.), Xanthocomus attenuatus (Casey, 1890) (=Xanthocomus concinnus (Casey, 1916), syn. nov.; Stilbus thoracicus Casey, 1916, syn. nov.; Stilbus quadrisetosus Casey, 1916, syn. nov.). One name, Olibrus sternalis Casey 1916, is resurrected from synonymy. Lectotypes are designated for 23 nominal species. One genus and two species are excluded from Phalacridae: Sternosternus Guillebeau 1894 (with its type and only species, S. grouvelleiGuillebeau 1894) and Parasemus parvopallidus Lea 1932, both of which belong in Hydrophilidae. All 34 resulting genera in the family Phalacridae are keyed, described, and illustrated. A phylogenetic hypothesis based on analysis of a matrix of 98 morphological characters was created using parsimony. Results of these analyses were not robust enough at deep levels to create a new subfamilial or tribal classification, but nine genus-groups have been hypothesized.

Iridaceae 'Out of Australasia'? Phylogeny, Biogeography, and Divergence Time Based on Plastid DNA Sequences

2008 ◽  
Vol 33 (3) ◽  
pp. 495-508 ◽  
Author(s):  
Peter Goldblatt ◽  
Aaron Rodriguez ◽  
M. P. Powell ◽  
Jonathan T. Davies ◽  
John C. Manning ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Secondary Growth ◽  
Divergence Time ◽  
Plastid Dna ◽  
Morphological Characters ◽  
Evolutionary Patterns ◽  
Related Family ◽  
The Family

The current infrafamilial taxonomy of the Iridaceae recognizes four subfamilies; Isophysidoideae (1: 1); Nivenioideae (6: ca. 92), Iridoideae (29: 890), and Crocoideae (29: 1032). Phylogenetic analyses of sequences of five plastid DNA regions, rbcL, rps4, trnL–F, matK, and rps16, confirm most aspects of this classification and the evolutionary patterns that they imply, importantly the sisiter relationship of Isophysidoideae to the remainder of the family and the monophyly of Iridoideae. Subfamily Nivenioideae is, however, paraphyletic; Crocoideae is consistently found nested within it, sister to the core Nivenioideae, the woody Klattia, Nivenia, and Witsenia. This clade is sister to Aristea, which in turn is sister to the Madagascan Geosiris, and then to the Australasian Patersonia. We treat Aristea, Geosiris, and Patersonia as separate subfamilies, Aristeoideae and the new Geosiridaceae and Patersonioideae, rendering Nivenioideae and Crocoideae monophyletic. The alternative, uniting a widely circumscribed Nivenioideae and Crocoideae, seems undesirable because Nivenioideae have none of the numerous synapomorphies of Crocoideae, and that subfamily includes more than half the total species of Iridaceae. Main synapomorphies of Crocoideae are: pollen operculate; exine perforate; ovule campylotropous; root xylem vessels with simple perforations; rootstock a corm; inflorescence usually a spike; plants deciduous. Four more derived features of Crocoideae are shared only with core Nivenioideae: flowers long-lived; perianth tube well developed; flowers sessile; and septal nectaries present. The genera of the latter subfamily are evergreen shrubs, have monocot-type secondary growth, tangentially flattened seeds, and the inflorescence unit is a binate rhipidium. The latter feature unites core Nivenioideae with Aristea, Geosiris, and Patersonia, which have fugaceous flowers and, with few exceptions, a blue perianth. Molecular-based phylogenetic trees using sequences from five plastid DNA regions now show discrete generic clusters within Crocoideae and Iridoideae, the foundation for the tribal classification. The five tribe classification of Iridoideae, initially based on morphological characters and subsequently supported by a four plastid DNA region sequence analysis, continues to receive support using additional DNA sequences. Application of molecular clock techniques to our phylogeny indicates that the Iridaceae differentiated in the late Cretaceous and diverged from the next most closely related family, Doryanthaceae circa 82 mya, thus during the Campanian. The Tasmanian Isophysis is the only extant member of the clade sister to the remainder of the Iridaceae, from which it may have diverged 66 mya, in the Maastrichtian. The generic phylogeny shows the proximal clades of the family are all Australasian, which corroborates past hypotheses that the Iridaceae originated in Antarctica-Australasia, although its subsequent radiation occurred elsewhere, notably in southern Africa and temperate and highland South America at the end of the Eocene or later.

Catalogue of Recent and fossil taxa of the family Architectonicidae Gray, 1850 (Mollusca: Gastropoda)

Zootaxa ◽  
2005 ◽  
Vol 1101 (1) ◽  
pp. 1 ◽  
Author(s):  
RÜDIGER BIELER ◽  
RICHARD E. PETIT
Keyword(s):  
Species Group ◽  
Family Group ◽  
Current Status ◽  
Marine Gastropod ◽  
Extant Species ◽  
The Family ◽  
Group 10

The marine gastropod family Architectonicidae (= Solariidae), commonly known as sundials, comprises about 140 worldwide extant species classified in 11 genera. More than ten times as many names are used in the literature for both Recent and fossil taxa, the latter dating from the Mesozoic (Paleozoic taxa were misinterpreted). Herein we catalog more than 1550 names that have appeared in print at the family-group (10), genus-group (137), and species-group levels (1408). Of the last, nearly 1100 are found to be nomenclatorially available or potentially available. An Appendix is included in which nomenclatural changes are made and/or commented upon. It is demonstrated that Solarium maculatum Link, 1807 was validly introduced and, as Architectonica maculata (Link, 1807), becomes the valid name for the species usually cited as A. picta (Philippi, 1849). The invalid introduction of Heliacus messanensis Bertolaso & Palazzi, 2000 is discussed. The emended spelling of the specific name in the binomen Solatisonax alleryi (G. Seguenza, 1876) is shown to be correctly accepted. Philippia lepida Bayer, 1942, Torinia gyrus depressiusculaBayer, 1848, Solarium subconcolor von Martens, 1880, Solarium conulus Weinkauff, 1868 and Solarium submoniliferum d’Orbigny, 1852 were proposed as replacement names for multiple preoccupied names and/or misidentifications. These are here restricted to avoid possible confusion. The history and current status of the similarly spelled and inconsistently used nomina Fluxiella and Fluxinella (as placed in Architectonicidae and/or Seguenziidae) are discussed.

Delimitation of the new tribe Parartocarpeae (Moraceae) is supported by a 333-gene phylogeny and resolves tribal level Moraceae taxonomy

Phytotaxa ◽  
2019 ◽  
Vol 388 (4) ◽  
pp. 253 ◽  
Author(s):  
NYREE J.C. ZEREGA ◽  
ELLIOT M. GARDNER
Keyword(s):  
Single Layer ◽  
Morphological Characters ◽  
Nuclear Genes ◽  
Target Enrichment ◽  
Gene Phylogeny ◽  
Genus Level ◽  
Phylogenetic Methods ◽  
The Family ◽  
New Tribe

Here we describe the new tribe, Parartocarpeae, within the Moraceae (mulberry family). The tribe comprises two small Malesian genera, Parartocarpus and Hullettia, and brings the total number of Moraceae tribes to seven. Evidence for this new designation comes from a phylogeny based on 333 nuclear genes sequenced using target enrichment via hybridization (hybseq). Morphological characters that set Parartocarpeae apart from other Moraceae tribes include the combination of the following characters: lateral nonamplexicaul stipules, spirally arranged leaves without annulate stipule scars, the presence of a single layer of involucral inflorescence bracts, and the lack of perianth tissue, wherein flowers are embedded in cavities of the receptacle. With the designation of Parartocarpeae, the tribe-level circumscription of Moraceae is now well-supported by phylogenetic methods. Because the phylogenetic markers employed here work well throughout Moraceae, they can facilitate much needed work at the genus level in the family.

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