scholarly journals Perspectives in Earthworm Molecular Phylogeny: Recent Advances in Lumbricoidea and Standing Questions

Diversity ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 30
Author(s):  
Daniel Fernández Marchán ◽  
Thibaud Decaëns ◽  
Jorge Domínguez ◽  
Marta Novo
Keyword(s):  
Molecular Phylogenetics ◽  
Morphological Characters ◽  
Reduced Representation ◽  
The Family ◽  
The Status ◽  
Molecular Phylogenetic ◽  
Terrestrial Habitats ◽  
Integrative Systematics ◽  
Representation Techniques ◽  
Targeted Enrichment

Earthworm systematics have been limited by the small number of taxonomically informative morphological characters and high levels of homoplasy in this group. However, molecular phylogenetic techniques have yielded significant improvements in earthworm taxonomy in the last 15 years. Several different approaches based on the use of different molecular markers, sequencing techniques, and compromises between specimen/taxon coverage and phylogenetic information have recently emerged (DNA barcoding, multigene phylogenetics, mitochondrial genome analysis, transcriptome analysis, targeted enrichment methods, and reduced representation techniques), providing solutions to different evolutionary questions regarding European earthworms. Molecular phylogenetics have led to significant advances being made in Lumbricidae systematics, such as the redefinition or discovery of new genera (Galiciandrilus, Compostelandrilus, Vindoboscolex, Castellodrilus), delimitation and revision of previously existing genera (Kritodrilus, Eophila, Zophoscolex, Bimastos), and changes to the status of subspecific taxa (such as the Allolobophorachaetophora complex). These approaches have enabled the identification of problems that can be resolved by molecular phylogenetics, including the revision of Aporrectodea, Allolobophora, Helodrilus, and Dendrobaena, as well as the examination of small taxa such as Perelia, Eumenescolex, and Iberoscolex. Similar advances have been made with the family Hormogastridae, in which integrative systematics have contributed to the description of several new species, including the delimitation of (formerly) cryptic species. At the family level, integrative systematics have provided a new genus system that better reflects the diversity and biogeography of these earthworms, and phylogenetic comparative methods provide insight into earthworm macroevolution. Despite these achievements, further research should be performed on the Tyrrhenian cryptic complexes, which are of special eco-evolutionary interest. These examples highlight the potential value of applying molecular phylogenetic techniques to other earthworm families, which are very diverse and occupy different terrestrial habitats across the world. The systematic implementation of such approaches should be encouraged among the different expert groups worldwide, with emphasis on collaboration and cooperation.

scholarly journals A taxonomic revision of the family Harrimaniidae (Hemichordata: Enteropneusta) with descriptions of seven species from the Eastern Pacific

Zootaxa ◽  
2010 ◽  
Vol 2408 (1) ◽  
pp. 1 ◽  
Author(s):  
C. DELAND ◽  
C. B. CAMERON ◽  
K. P. RAO ◽  
W. E. RITTER ◽  
T. H. BULLOCK
Keyword(s):  
New Species ◽  
Taxonomic Revision ◽  
Morphological Characters ◽  
Eastern Pacific ◽  
Nomen Nudum ◽  
Phylogenetic Hypothesis ◽  
Number Of Species ◽  
Dichotomous Key ◽  
The Family ◽  
The Status

The family Harrimaniidae (Hemichordata: Enteropneusta) is revised on the basis of morphological characters. The number of harrimaniid genera is increased to nine by the addition of Horstia n. gen., Mesoglossus n. gen., Ritteria n. gen. and Saxipendium, a genus previously assigned to the monospecific family Saxipendiidae. The number of species is increased to 34, resulting from the description of five new species from the eastern Pacific — Horstia kincaidi, Mesoglossus intermedius, M. macginitiei, Protoglossus mackiei and Ritteria ambigua. A description is supplied for a sixth harrimaniid species, Stereobalanus willeyi Ritter & Davis, 1904, which previously had the status of a nomen nudum. Four harrimaniids previously assigned to the genus Saccoglossus are transfered to the genus Mesoglossus — M. bournei, M. caraibicus, M. gurneyi and M. pygmaeus, while Saccoglossus borealis is reassigned to the genus Harrimania. Notes on habitat and zoogeography are included for the seven foregoing species and a table of diagnostic characters for existing and new species and a dichotomous key to the enteropneust families and harrimaniid genera are provided. Finally, a phylogenetic hypothesis concerning the Harrimaniidae is postulated, with discussion on the evolution of the group.

The Fossil Record of the Pancrustacea

2020 ◽  
pp. 21-52 ◽  
Author(s):  
Thomas A. Hegna ◽  
Javier Luque ◽  
Joanna M. Wolfe
Keyword(s):  
Fossil Record ◽  
Hydrothermal Vents ◽  
Molecular Phylogenetics ◽  
Imaging Techniques ◽  
Extant Species ◽  
Evolutionary Studies ◽  
Molecular Phylogenetic ◽  
Terrestrial Habitats ◽  
Molecular Phylogenetic Data

Fossils are critically important for evolutionary studies as they provide the link between geological ages and the phylogeny of life. The Pancrustacea are an incredibly diverse clade, representing over 800,000 described extant species, encompassing a variety of familiar and unfamiliar forms, such as ostracods, tongue worms, crabs, lobsters, shrimps, copepods, barnacles, branchiopods, remipedes, and insects. Having colonized nearly every environment on Earth, from hydrothermal vents to terrestrial habitats, they have a diverse fossil record dating back to the Cambrian (540–485 Ma). The quality of the fossil record of each clade is variable and related to their lifestyle (e.g., free-living versus parasitic, benthic versus pelagic) and the degree of mineralization of their cuticle. We review the systematics, morphology, preservation, and paleoecology of pancrustacean fossils; each major clade is discussed in turn, and, where possible, fossil systematics are compared with more recent data from molecular phylogenetics. We show that the three epic clades of the Pancrustacea—Allotriocarida, Multicrustacea, and Oligostraca—all have Cambrian roots, but the diversification of those clades did not take place until the Middle and Late Paleozoic. We also address the potential affinities of three “problematic” clades: euthycarcinoids, thylacocephalans, and cyclids. We conclude by assessing the future of pancrustacean paleobiology, discussing new morphological imaging techniques and further integration with growing molecular phylogenetic data.

scholarly journals Marrying molecules and morphology: first steps towards a reevaluation of solariellid genera (Gastropoda: Trochoidea) in the light of molecular phylogenetic studies

2020 ◽  
Vol 86 (1) ◽  
pp. 1-26
Author(s):  
S T Williams ◽  
Y Kano ◽  
A Warén ◽  
D G Herbert
Keyword(s):  
Type Species ◽  
Morphological Characters ◽  
Shell Shape ◽  
Molecular Systematic ◽  
The Past ◽  
Phylogenetic Studies ◽  
Clade B ◽  
The Family ◽  
Molecular Phylogenetic ◽  
Anatomical Characters

ABSTRACT The assignment of species to the vetigastropod genus Solariella Wood, 1842, and therefore the family Solariellidae Powell, 1951, is complicated by the fact that the type species (Solariella maculata Wood, 1842) is a fossil described from the Upper Pliocene. Assignment of species to genera has proved difficult in the past, and the type genus has sometimes acted as a ‘wastebasket’ for species that cannot easily be referred to another genus. In the light of a new systematic framework provided by two recent publications presenting the first molecular phylogenetic data for the group, we reassess the shell characters that are most useful for delimiting genera. Shell characters were previously thought to be of limited taxonomic value above the species level, but this is far from the case. Although overall shell shape is not a reliable character, our work shows that shell characters, along with radular and anatomical characters, are useful for assigning species to genera. Sculpture of the early teleoconch (the region immediately following the protoconch) and the columella are particularly useful characters that have not been used regularly in the past to distinguish genera. However, even with the combination of all morphological characters used in this study (shell, radular and eye), a few species are still difficult to assign to genera and in such cases molecular systematic data are essential. In the present study, we discuss 13 genera—12 of which were recovered as well-supported clades in recent molecular systematic studies—and provide morphological characters to distinguish them. We describe several new taxa: Chonospeira n. gen. (referred to as ‘clade B’ in previous molecular systematic studies), Phragmomphalina n. gen. (Bathymophila in part in molecular systematic studies) and Phragmomphalina vilvensi n. sp. (type species of Phragmomphalina n. gen.). We synonymize Hazuregyra Shikama, 1962 with Minolia A. Adams, 1860, Minolia subangulata Kuroda & Habe, 1952 with Minolia punctata A. Adams, 1860 and M. gemmulata Kuroda & Habe, 1971 with M. shimajiriensis (MacNeil, 1960). We also present the following new combinations: Bathymophila bairdii (Dall, 1889), B. dawsoni (Marshall, 1979), B. regalis (Marshall, 1999), B. wanganellica (Marshall, 1999), B. ziczac (Kuroda & Habe in Kuroda, Habe & Oyama, 1971), Chonospeira nuda (Dall, 1896), C. iridescens (Habe, 1961), C. ostreion (Vilvens, 2009), C. strobilos (Vilvens, 2009), Elaphriella corona (Lee & Wu, 2001), E. diplax (Marshall, 1999), E. meridiana (Marshall, 1999), E. olivaceostrigata (Schepman, 1908), E. opalina (Shikama & Hayashi, 1977), Ilanga norfolkensis (Marshall, 1999), I. ptykte (Vilvens, 2009), I. zaccaloides (Vilvens, 2009), Minolia shimajiriensis (MacNeil, 1960), M. watanabei (Shikama, 1962), Phragmomphalina alabida (Marshall, 1979), P. diadema (Marshall, 1999), P. tenuiseptum (Marshall, 1999), Spectamen euteium (Vilvens, 2009), S. basilicum (Marshall, 1999), S. exiguum (Marshall, 1999) and S. flavidum (Marshall, 1999).

scholarly journals In situmorphometric survey elucidates the evolutionary systematics of the EurasianHimantoglossumclade (Orchidaceae: Orchidinae)

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2893 ◽  
Author(s):  
Richard M. Bateman ◽  
Attila Molnár V. ◽  
Gábor Sramkó
Keyword(s):  
Molecular Phylogenetics ◽  
Morphological Characters ◽  
Morphometric Character ◽  
Clinal Variation ◽  
Plant Vigour ◽  
Parallel Acquisition ◽  
The Status ◽  
Show Evidence ◽  
Conservation Concern ◽  
Vegetative Characters

Background and AimsThe charismaticHimantoglossum s.l.clade of Eurasian orchids contains an unusually large proportion of taxa that are of controversial circumscriptions and considerable conservation concern. Whereas our previously published study addressed the molecular phylogenetics and phylogeography of every named taxon within the clade, here we use detailed morphometric data obtained from the same populations to compare genotypes with associated phenotypes, in order to better explore taxonomic circumscription and character evolution within the clade.MethodsBetween one and 12 plants found in 25 populations that encompassed the entire distribution of theHimantoglossum s.l.clade were measuredin situfor 51 morphological characters. Results for 45 of those characters were subjected to detailed multivariate and univariate analyses.Key ResultsMultivariate analyses readily separate subgenusBarliaand subgenusComperiafrom subgenusHimantoglossum, and also the early-divergentH. formosumfrom the less divergent remainder of subgenusHimantoglossum. The sequence of divergence of these four lineages is confidently resolved. Our experimental approach to morphometric character analysis demonstrates clearly that phenotypic evolution withinHimantoglossumis unusually multi-dimensional.ConclusionsDegrees of divergence between taxa shown by morphological analyses approximate those previously shown using molecular analyses.Himantoglossum s.l. is readily divisible into three subgenera. The three sections of subgenusHimantoglossum—hircinum,caprinumandformosum—are arrayed from west to east with only limited geographical overlap. At this taxonomic level, their juxtaposition combines with conflict between contrasting datasets to complicate attempts to distinguish between clinal variation and the discontinuities that by definition separatebona fidespecies. All taxa achieve allogamy via food deceit and have only weak pollinator specificity. Artificial crossing demonstrates that intrinsic sterility barriers are weak. Although we have found evidence of gene flow among and within the three sections of subgenusHimantoglossum, reports of natural hybrids are surprisingly rare, probably because putative parents are sufficiently similar to questionably warrant the status of species. Phenological separation and increased xeromorphy characterise the origin of subgenusBarlia. Several individual morphological characters show evidence of parallel acquisition, and loss of features is especially frequent in floral markings among members of sectioncaprinum. Detailed patterns of gain and loss demonstrate that several different categories of flower markings are inherited independently. Along with the dimensions of labellar lobes, these pigmentation characters have been over-emphasised in previous taxonomic treatments. Increased plant vigour was a crucial element of the origin of the genus, but vegetative characters underwent remarkably little subsequent evolution. Attempts to reconstruct hypothetical ancestors at internal nodes of the phylogeny are weakened by (a) uncertain placement ofSteveniellaas sister toHimantoglossum s.l.and (b) uncertain relationships among subtly different putative species within sectioncaprinum. Nonetheless, heterochronic/allometric trends, ultimately limited by functional constraints, clearly dictate transitions between contrasting flower sizes and complex labellum shapes.

Molecular phylogenetic analyses and morphological variation point to taxonomic problems among four genera of parasitoid doryctine wasps (Hymenoptera : Braconidae)

2015 ◽  
Vol 29 (6) ◽  
pp. 591 ◽  
Author(s):  
Marco Gebiola ◽  
Antonio P. Garonna ◽  
Umberto Bernardo ◽  
Sergey A. Belokobylskij
Keyword(s):  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Molecular Evidence ◽  
A Posteriori ◽  
Morphological Examination ◽  
Ongoing Effort ◽  
The Status ◽  
Molecular Phylogenetic

Doryctinae (Hymenoptera : Braconidae) is a large and diverse subfamily of parasitic wasps that has received much attention recently, with new species and genera described and phylogenies based on morphological and/or molecular data that have improved higher-level classification and species delimitation. However, the status of several genera is still unresolved, if not controversial. Here we focus on two related groups of such genera, Dendrosoter Wesmael–Caenopachys Foerster and Ecphylus Foerster–Sycosoter Picard & Lichtenstein. We integrated morphological and molecular (COI and 28S–D2 genes) evidence to highlight, by phylogenetic analyses (maximum likelihood and Bayesian) and a posteriori morphological examination, previously overlooked variation, which is here illustrated and discussed. Monophyly of Dendrosoter and Caenopachys and the presence of synapomorphic morphological characters support synonymy of Caenopachys under Dendrosoter. Low genetic differentiation and high variability for putatively diagnostic morphological characters found in both C. hartigii (Ratzeburg) and C. caenopachoides (Ruschka) supports synonymy of D. caenopachoides under D. hartigii, syn. nov. Morphological and molecular evidence together also indicate independent generic status for Sycosoter, stat. rev., which is here resurrected. This work represents a further advancement in the framework of the ongoing effort to improve systematics and classification of the subfamily Doryctinae.

scholarly journals On the systematic position of the genus Timmiella (Dicranidae, Bryopsida) and its allied genera, with the description of a new family Timmiellaceae

Phytotaxa ◽  
2014 ◽  
Vol 181 (3) ◽  
pp. 151 ◽  
Author(s):  
Yuya Inoue ◽  
Hiromi Tsubota
Keyword(s):  
Phylogenetic Analysis ◽  
Morphological Characters ◽  
Systematic Position ◽  
Molecular Phylogenetic Analysis ◽  
New Family ◽  
Leaf Surfaces ◽  
The Family ◽  
Molecular Phylogenetic

Based on our molecular phylogenetic analysis of haplolepideous mosses with concatenated sequences of chloroplast rps4 and rbcL genes, a new family Timmiellaceae is erected to accommodate the genera Timmiella and Luisierella, both of which have been formerly included in the family Pottiaceae.  The family Timmiellaceae is resolved as a second-branching clade together with Distichium (Distichiaceae) within the Dicranidae (haplolepideous moss) lineages and phylogenetically distinct from the Pottiaceae.  Reassessment of morphological characters suggests that a combination of the characters: 1) adaxially bulging and abaxially flat leaf surfaces, 2) sinistrorse or straight peristomes, when present, and 3) sinistrorsely arranged operculum cells is unique to Timmiellaceae and discriminates it from other haplolepideous moss families.

The Idoteidae (Crustacea: Isopoda: Valvifera) of the shallow waters of the northeastern North Pacific Ocean

1990 ◽  
Vol 68 (12) ◽  
pp. 2649-2687 ◽  
Author(s):  
F. Rafi ◽  
Diana R. Laubitz
Keyword(s):  
North Pacific ◽  
North Pacific Ocean ◽  
Morphological Characters ◽  
Generic Level ◽  
Additional Species ◽  
The Family ◽  
Juan De Fuca ◽  
The Status ◽  
Juan De Fuca Strait ◽  
Systematic Importance

The distribution of the northeastern North Pacific Idoteidae reflects the general eurytopy in the shallow marine environment of the component species. The family is represented by four genera and 20 species in the region between Juan de Fuca Strait, Washington, and Prince William Sound, Alaska. Collections studied from this area contained 16 species of idoteids, of which 3 (Idotea (Pentidotea) recta, Synidotea cornuta, and S. minuta) are new; the new species are fully illustrated and described. The status of nine additional species recorded in the literature from the area is discussed, and four of them are diagnosed and included in the keys. The morphological characters of the four genera were examined in detail and their systematic importance is discussed. All the appendages surveyed showed differences at least at the generic level.

Pseudaphelenchus yukiae n. gen., n. sp. (Tylenchina: Aphelenchoididae) associated with Cylindrotermes macrognathus (Termitidae: Termitinae) in La Selva, Costa Rica

Nematology ◽  
2009 ◽  
Vol 11 (6) ◽  
pp. 869-881 ◽  
Author(s):  
Natsumi Kanzaki ◽  
Robin M. Giblin-Davis ◽  
Rudolf H. Scheffrahn ◽  
Barbara J. Center ◽  
Kerrie A. Davies
Keyword(s):  
Costa Rica ◽  
New Genus ◽  
Morphological Characters ◽  
Subterranean Termite ◽  
La Selva ◽  
The Family ◽  
Phylogenetic Status ◽  
Molecular Phylogenetic ◽  
Definition Of ◽  
Ribosomal Dna Sequence

Abstract A species of aphelenchoidid nematode was isolated from a subterranean termite, Cylindrotermes macrognathus, during a survey of termite-associated nematodes in a conserved forest in La Selva, Costa Rica. The nematode was morphologically intermediate between the families Aphelenchidae and Aphelenchoididae, i.e., the nematode had a true bursa supported by bursal limb-like genital papillae but lacked a clear pharyngeal isthmus. The molecular phylogenetic status of the new nematode among tylenchid, cephalobid, panagrolaimid, aphelenchid and aphelenchoidid genera was analysed based on ca 1.2 kb of SSU ribosomal DNA sequence and the inferred position was basal to the family Aphelenchoididae. It was clearly not part of the clade containing the genus Aphelenchus (=Aphelenchidae). This nematode is described herein as Pseudaphelenchus yukiae n. gen., n. sp., and the family definition of Aphelenchoididae is emended to include the unique morphological characters of this new genus. The molecular phylogenetic analysis supported the paraphyly of the three Aphelenchoidinae genera Aphelenchoides, Laimaphelenchus and Schistonchus and the monophyly of Ektaphelenchinae, Seinura (Seinurinae) and Noctuidonema (Acugutturinae). However, many more representatives are needed to resolve the family-genus level phylogeny of Aphelenchoididae.

scholarly journals An updated infrageneric classification of the oaks: review of previous taxonomic schemes and synthesis of evolutionary patterns

2017 ◽  
Author(s):  
Thomas Denk ◽  
Guido W. Grimm ◽  
Paul S. Manos ◽  
Min Deng ◽  
Andrew Hipp
Keyword(s):  
Molecular Phylogenetics ◽  
Morphological Characters ◽  
Evolutionary Patterns ◽  
Traditional Concept ◽  
Infrageneric Classification ◽  
Systematic Scheme ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Phylogenetic Lineages

In this paper, we review major classification schemes proposed for oaks by John Claudius Loudon, Anders Sandøe Ørsted, William Trelease, Otto Karl Anton Schwarz, Aimée Antoinette Camus, Yuri Leonárdovich Menitsky, and Kevin C. Nixon. Classifications of oaks (Fig. 1) have thus far been based entirely on morphological characters. They differed profoundly from each other because each taxonomist gave a different weight to distinguishing characters; often characters that are homoplastic in oaks. With the advent of molecular phylogenetics our view has considerably changed. One of the most profound changes has been the realisation that the traditional split between the East Asian subtropical to tropical subgenus Cyclobalanopsis and the subgenus Quercus that includes all other oaks is artificial. The traditional concept has been replaced by that of two major clades, each comprising three infrageneric groups: a Palearctic-Indomalayan clade including Group Ilex (Ilex oaks), Group Cerris (Cerris oaks) and Group Cyclobalanopsis (cycle-cup oaks), and a predominantly Nearctic clade including Group Protobalanus (intermediate or golden cup oaks), Group Lobatae (red oaks) and Group Quercus (white oaks, with most species in America and some 30 species in Eurasia). The main morphological feature characterising these phylogenetic lineages is pollen morphology, a character overlooked in traditional classifications. This realisation, along with the now available (molecular-)phylogenetic framework, opens new avenues for biogeographic, ecological and evolutionary studies and a re-appraisal of the fossil record. We provide an overview about recent advances in these fields and outline how the results of these studies contribute to the establishment of a unifying systematic scheme of oaks. Ultimately, we propose an updated classification of Quercus recognising two subgenera with eight sections. This classification considers morphological traits, molecular-phylogenetic relationships, and the evolutionary history of one of the most important temperate woody plant genera.

Molecular phylogenetics of snailfishes (Cottoidei: Liparidae) based on MtDNA and RADseq genomic analyses, with comments on selected morphological characters

Zootaxa ◽  
2019 ◽  
Vol 4642 (1) ◽  
pp. 1-79 ◽  
Author(s):  
JAMES WILDER ORR ◽  
INGRID SPIES ◽  
DUANE E. STEVENSON ◽  
GARY C. LONGO ◽  
YOSHIAKI KAI ◽  
...  
Keyword(s):  
Molecular Phylogenetics ◽  
Sequence Data ◽  
Morphological Characters ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Genome Wide ◽  
The Pacific ◽  
The Family ◽  
Genomic Analyses ◽  
Gene Coi

Phylogenetic relationships of snailfishes of the family Liparidae were analyzed on the basis of two sets of molecular sequence data: one from the mitochondrial DNA cytochrome c oxidase subunit one gene (COI) and another from restriction-site associated genome-wide sequences (RADseq). The analysis of COI sequence data from at least 122 species of 18 genera from the Pacific, Atlantic, and Southern oceans resulted in a moderately well-resolved phylogeny among the major clades, albeit with significant polytomy among central clades. Nectoliparis was the sister of all other members of the family, followed by Liparis. Liparis, Careproctus, and Paraliparis were paraphyletic. Liparis was recovered in two closely related clades, with L. fucensis sister of all other liparids except Nectoliparis, and both Careproctus and Paraliparis were each recovered among at least three widely separated clades. The RADseq analysis of 26 species of 11 genera from the eastern North Pacific strongly confirmed the overall results of the COI analysis, with the exception of the paraphyly of Liparis due to the absence of L. fucensis. Our results show that the pelvic disc has been independently lost multiple times and the pectoral-fin girdle has been independently reduced in multiple lineages. 

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