Molecular diversity and species delimitation in the family Gasteruptiidae (Hymenoptera: Evanioidea)

Genome ◽  
2020 ◽  
pp. 1-12
Author(s):  
Ben A. Parslow ◽  
Michael P. Schwarz ◽  
Mark I. Stevens
Keyword(s):  
Species Delimitation ◽  
Sequence Data ◽  
Molecular Data ◽  
Multiple Parameters ◽  
Operational Taxonomic Units ◽  
The Family ◽  
Molecular Phylogenetic ◽  
Taxonomic Uncertainty ◽  
Traditional Taxonomy ◽  
Morphological Species

Gasteruptiidae Ashmead is an easily recognised family of wasps with ∼589 described species worldwide. Although well characterised by traditional taxonomy, multiple authors have commented on the extreme morphological uniformity of the group, making species-level identification difficult. This problem is enhanced by the lack of molecular data and molecular phylogenetic research for the group. We used 187 cytochrome c oxidase subunit I (COI) barcodes to explore the efficiency of sequence data to delimitate species in Gasteruptiidae. We undertook a graphical and discussion-based comparison of six methods for species delimitation, with the success of methods judged based on known species boundaries and morphology. Both distance-based (ABGD and jMOTU threshold analysis) and tree-based (GMYC and PTP) methods compared across multiple parameters recovered variable molecular operational taxonomic units (MOTUs), ranging from 55 to 123 MOTUs. Tree-based methods tended to split known morphological species less than distance-based methods, with the single-threshold GMYC method the most concordant with known morphospecies. Our results suggest that the incorporation of molecular species delimitation techniques provides a powerful tool to assist in the interpretation of species and help direct informed decisions with taxonomic uncertainty in the family.

The status of Myriangiaceae (Dothideomycetes)

Phytotaxa ◽  
2014 ◽  
Vol 176 (1) ◽  
pp. 219 ◽  
Author(s):  
ASHA J. DISSANAYAKE ◽  
RUVISHIKA S. JAYAWARDENA ◽  
SARANYAPHAT BOONMEE ◽  
KASUN M. THAMBUGALA ◽  
QING TIAN ◽  
...  
Keyword(s):  
Sequence Data ◽  
Molecular Data ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
The Family ◽  
The Status ◽  
Sexual State ◽  
Morphological And Molecular Data ◽  
Asexual State ◽  
Molecular Characters

The family Myriangiaceae is relatively poorly known amongst the Dothideomycetes and includes genera which are saprobic, epiphytic and parasitic on the bark, leaves and branches of various plants. The family has not undergone any recent revision, however, molecular data has shown it to be a well-resolved family closely linked to Elsinoaceae in Myriangiales. Both morphological and molecular characters indicate that Elsinoaceae differs from Myriangiaceae. In Elsinoaceae, small numbers of asci form in locules in light coloured pseudostromata, which form typical scab-like blemishes on leaf or fruit surfaces. The coelomycetous, “Sphaceloma”-like asexual state of Elsinoaceae, form more frequently than the sexual state; conidiogenesis is phialidic and conidia are 1-celled and hyaline. In Myriangiaceae, locules with single asci are scattered in a superficial, coriaceous to sub-carbonaceous, black ascostromata and do not form scab-like blemishes. No asexual state is known. In this study, we revisit the family Myriangiaceae, and accept ten genera, providing descriptions and discussion on the generic types of Anhellia, Ascostratum, Butleria, Dictyocyclus, Diplotheca, Eurytheca, Hemimyriangium, Micularia, Myriangium and Zukaliopsis. The genera of Myriangiaceae are compared and contrasted. Myriangium duriaei is the type species of the family, while Diplotheca is similar and may possibly be congeneric. The placement of Anhellia in Myriangiaceae is supported by morphological and molecular data. Because of similarities with Myriangium, Ascostratum (A. insigne), Butleria (B. inaghatahani), Dictyocyclus (D. hydrangea), Eurytheca (E. trinitensis), Hemimyriangium (H. betulae), Micularia (M. merremiae) and Zukaliopsis (Z. amazonica) are placed in Myriangiaceae. Molecular sequence data from fresh collections is required to confirm the relationships and placement of the genera in this family.

Species delimitation of the northeastern Anatolian Symphytum (Boraginaceae) taxa

Phytotaxa ◽  
2021 ◽  
Vol 516 (3) ◽  
Author(s):  
KURTULUŞ ÖZGİŞİ ◽  
BURCU TARIKAHYA-HACIOĞLU
Keyword(s):  
Species Delimitation ◽  
Sequence Data ◽  
Molecular Data ◽  
Morphological Data ◽  
Infrageneric Classification ◽  
Number Of Species ◽  
Morphological Studies ◽  
Statistical Parsimony ◽  
Taxonomical Status ◽  
Parsimony Network Analysis

Symphytum is regarded one of the most complicated genera in terms of the classification of its members among the Boraginaceae. In addition to different infrageneric classification methods, several species complex or aggregates have been proposed to deal with the taxonomical problem of genus members. Symphytum asperum aggregate was first introduced by Kurtto, who proposed six taxa within this aggregate. However, according to further studies by different researchers based on morphological data, total number of species of the complex was variable. The number of species was reduced to three, comprising S. asperum, S. savvalense, and S. sylvaticum, after the phylogenetic and morphological studies of Tarıkahya-Hacıoğlu and Erik. However, the taxonomical status of some of these species (i.e., S. savvalense and S. sylvaticum, and S. sepulcrale), which was assigned as a member of this complex by Kurtto, has been regarded as unresolved. To solve this uncertainty, different species delimitation methods were used, including statistical parsimony network analysis (TCS), generalized mixed Yule coalescent (GMYC), and Bayesian Phylogenetics and Phylogeography (BPP) of the ITS, trnL-F and trnS-G sequence data. In addition to members of this complex, S. ibericum, which is phylogenetically nested within the S. asperum aggregate, was also used. The TCS and GMYC analyses demonstrated more complicated clusters, whereas high posterior probabilities of BPP clusters were more compatible with the morphological data. In accordance with the morphological approach of Tarıkahya-Hacıoğlu and Erik, the species delimitation analyses based on molecular data support the recognition of S. asperum, S. ibericum, S. savvalense, and S. sylvaticum as different species.

Molecular phylogenetic relationships of Metastrongylus nematodes with emphasis on specimens from domestic pigs in Vietnam

2021 ◽  
Vol 95 ◽  
Author(s):  
N.V. Tuyen ◽  
N.T.K. Lan ◽  
P.N. Doanh
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Molecular Data ◽  
Global Scale ◽  
Single Infection ◽  
Parasitic Nematodes ◽  
Nucleotide Sequence Data ◽  
Wild Boars ◽  
Domestic Pigs ◽  
Molecular Phylogenetic

Abstract Lungworms of the genus Metastrongylus are parasitic nematodes in the respiratory tract of swine. Although they infect both wild boars and domestic pigs, studies on Metastrongylus infections in wild boars in Europe, the Americas and Africa are numerous, while those in domestic pigs are few. There are several studies analysing the molecular phylogenetic relationships of few individual Metastrongylus species with other nematode taxa, but there are no studies on the phylogenetic relationships of species within the genus Metastrongylus. In Southeast Asia, reports on swine lungworms are extremely scarce and do not include any nucleotide sequence data. Therefore, the aim of the present study is to survey Metastrongylus infection in domestic pigs raised in Dien Bien Province, Northern Vietnam, and to analyse the molecular phylogenetic relationships of Metastrongylus species. Based on morphological and molecular data, we identified two species: Metastrongylus apri and Metastrongylus pudendotectus. The prevalence of the former species was found to be significantly higher than the latter one (24.1% vs. 2.3%). We observed pigs exhibiting a coinfection with the two lungworm species or a single infection with only M. apri. However, we did not observe any pigs being infected with just M. pudendotectus. Vietnamese Metastrongylus specimens showed slight morphological and molecular differences compared to those from other countries. The molecular analyses revealed a close genetic relationship between M. apri and Metastrongylus salmi, while both these species were far distant from M. pudendotectus. The present study highlights the needs for further studies to clarify the morphological features and ecological and phylogenetic relationships of Metastrongylus species at the global scale.

Species delimitation and nematode biodiversity: phylogenies rule

Nematology ◽  
2002 ◽  
Vol 4 (5) ◽  
pp. 615-625 ◽  
Author(s):  
Steven Nadler
Keyword(s):  
Species Delimitation ◽  
Sequence Data ◽  
Molecular Data ◽  
Gene Trees ◽  
California Sea Lions ◽  
Separate Species ◽  
Nucleotide Sequence Data ◽  
Sea Lions ◽  
Multiple Loci ◽  
Fur Seals

AbstractPractitioners of nematode taxonomy have rarely been explicit about what species represent or how data are being used to delimit species prior to their description. This lack of explicitness reflects the broader species problem common to all biology: there is no universally accepted idea of what species are and, as a consequence, scientists disagree on how to go about finding species in nature. However, like other biologists, nematologists seem to agree that species are real and discrete units in nature, and that they result from descent with modification. This evolutionary perspective provides a conceptual framework for nematologists to view species as independent evolutionary lineages, and provides approaches for their delimitation. Specifically, species may be delimited scientifically by methods that can test the hypothesis of lineage independence. For sequence data, such hypothesis testing should be based on sampling many individual organisms for multiple loci to avoid mistaking tokogeny and gene trees as evidence of species. Evolutionary approaches to analysing data and delimiting species avoid the inherent pitfalls in approaches that use all observed sequence differences to define species through calculation of a genetic distance. To illustrate evolutionary species delimitation, molecular data are used to test the hypothesis that hookworms parasitic in northern fur seals and in California sea lions represent separate species. The advantages and potential caveats of employing nucleotide sequence data for species delimitation are discussed, and the merits of evolutionary approaches are contrasted to inherent problems in similarity-based methods.

A revision of the Leptogium saturninum group in North America

2016 ◽  
Vol 48 (5) ◽  
pp. 387-421 ◽  
Author(s):  
Daphne F. STONE ◽  
James W. HINDS ◽  
Frances L. ANDERSON ◽  
James C. LENDEMER
Keyword(s):  
North American ◽  
Morphological Study ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Lower Surface ◽  
Molecular Data ◽  
The North ◽  
Molecular Phylogenetic ◽  
Nrits Sequence

AbstractA revision of the North American members of the Leptogium saturninum group (i.e. species with long lower-surface hairs, isidia, and usually smooth upper surface) is presented based on molecular phylogenetic analyses of mtSSU and nrITS sequence data, together with an extensive morphological study. Three species supported by both molecular and morphological characteristics are recognized: L. acadiense sp. nov. (distinguished by granular saturninum-type isidia, medulla composed of irregularly arranged or perpendicular hyphae), L. cookii sp. nov. (distinguished by cylindrical saturninum-type isidia) and L. hirsutum (distinguished by hirsutum-type isidia and medulla composed of loosely intertwined hyphae). One species supported by morphological characteristics, but for which no molecular data could be generated, is also recognized: L. compactum sp. nov. (distinguished by hirsutum-type isidia and medulla composed of tightly packed hyphae). Finally, L. saturninum (distinguished by granular saturninum-type isidia and medulla composed of perpendicular and parallel hyphae) is supported by morphological characteristics but molecular data from geographically diverse populations, including those near the type locality, indicate that the morphologically defined species is paraphyletic. Leptogium burnetiae is excluded from North American based on morphological study of the type. The species are described and illustrated in detail, and are distinguished morphologically by their isidium development, morphology of mature isidia, and pattern of hyphae in the medulla in transverse sections near lobe margins. A key to the members of the L. saturninum group and related species is also presented.

Molecular data allow to elucidate the taxonomic placement of some Umbelliferae from Middle Asia and Afghanistan (Pinacantha, Ladyginia, Peucedanum mogoltavicum)

Phytotaxa ◽  
2018 ◽  
Vol 350 (1) ◽  
pp. 42 ◽  
Author(s):  
GALINA V. DEGTJAREVA ◽  
MICHAEL G. PIMENOV ◽  
TAHIR H. SAMIGULLIN
Keyword(s):  
Phylogenetic Tree ◽  
Dna Sequence ◽  
Sequence Data ◽  
Molecular Data ◽  
Systematic Position ◽  
New Combination ◽  
Dna Sequence Data ◽  
Middle Asia ◽  
Molecular Phylogenetic Tree ◽  
Molecular Phylogenetic

The systematic position of three Apiaceae-Apioideae taxa, Pinacantha porandica, Ladyginia bucharica and Peucedanum mogoltavicum, from Middle Asia and Afghanistan, is clarified based on nrITS DNA sequence data. In the molecular phylogenetic tree, the monotypic Pinacantha is placed in unresolved position within the Ferulinae. Although there is no morphological information on essential characters, we propose a new position of Pinacantha porandica within the genus Ferula. As a result a new combination Ferula porandica is proposed, with a new section Pinacantha to accommodate it. The attribution of Peucedanum mogoltavicum to Ferula has been confirmed, its correct name being Ferula lithophila. The genus Ladyginia should not be included in Ferula, its closest relatives being Mozaffariania and Glaucosciadium from the Glaucosciadium Clade.

Across Lydekker's Line - first report of mite harvestmen (Opiliones : Cyphophthalmi : Stylocellidae) from New Guinea

2007 ◽  
Vol 21 (3) ◽  
pp. 207 ◽  
Author(s):  
Ronald M. Clouse ◽  
Gonzalo Giribet
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
New Guinea ◽  
Single Male ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
The Family ◽  
Biogeographic Region ◽  
Molecular Phylogenetic ◽  
History Of

Opiliones (harvestmen) in the suborder Cyphophthalmi are not known to disperse across oceans and each family in the suborder is restricted to a clear biogeographic region. While undertaking a revisionary study of the South-east Asian family Stylocellidae, two collections of stylocellids from New Guinea were noted. This was a surprising find, since the island appears never to have had a land connection with Eurasia, where the rest of the family members are found. Here, 21 New Guinean specimens collected from the westernmost end of the island (Manokwari Province, Indonesia) are described and their relationships to other cyphophthalmids are analysed using molecular sequence data. The specimens represent three species, Stylocellus lydekkeri, sp. nov., S. novaguinea, sp. nov. and undescribed females of a probable third species, which are described and illustrated using scanning electron microscope and stereomicroscope photographs. Stylocellus novaguinea, sp. nov. is described from a single male and it was collected with a juvenile and the three females of the apparent third species. Molecular phylogenetic analyses indicate that the new species are indeed in the family Stylocellidae and they therefore reached western New Guinea by dispersing through Lydekker’s line – the easternmost limit of poor dispersers from Eurasia. The New Guinean species may indicate at least two episodes of oceanic dispersal by Cyphophthalmi, a phenomenon here described for the first time. Alternatively, the presence in New Guinea of poor dispersers from Eurasia may suggest novel hypotheses about the history of the island.

Mitochondrial sequence data clarify species concepts in the Cyclocephala mafaffa species complex (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini)

Zootaxa ◽  
2020 ◽  
Vol 4772 (1) ◽  
pp. 89-110
Author(s):  
MATTHEW R. MOORE ◽  
STEFANI M. HARRISON ◽  
RONALD D. CAVE ◽  
MARC A. BRANHAM
Keyword(s):  
Species Complex ◽  
Gap Analysis ◽  
Sequence Data ◽  
Species Concepts ◽  
Neighbor Joining ◽  
The West ◽  
Research Attention ◽  
Operational Taxonomic Units ◽  
Floral Visitation ◽  
Morphological Species

The speciose genus Cyclocephala Dejean (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini) has attracted research attention due to their diversity, agroeconomic importance, and floral visitation habits. Uniquely among Cyclocephala species, C. mafaffa Burmeister and C. deceptor (Casey), two nearly identical species, are diagnosed by a pronotal character: beaded or not beaded basal pronotal margin. We evaluated these morphological species hypotheses with a phylogenetic analysis of 12S and COI, neighbor-joining analysis, and several single-locus species delimitation procedures (automatic barcode gap analysis and three Poisson tree processes analyses). Together, these analyses supported the species concepts for C. deceptor and C. mafaffa. Delimitation procedures supported several distinct molecular operational taxonomic units among these taxa. We consider the separation of C. deceptor and C. mafaffa to be valid. We conservatively synonymize the West Indian subspecies C. mafaffa grandis Burmeister under C. mafaffa and offer a discussion on subspecific concepts in Cyclocephalini. We designate the lectotype of Stigmalia deficiens Casey. Implications of this study for other geographically widespread cyclocephalines or species with variable pronotal morphology are discussed. 

scholarly journals DNA Barcoding: Mixed results for big-headed flies (Diptera: Pipunculidae)

Zootaxa ◽  
2007 ◽  
Vol 1423 (1) ◽  
pp. 1-26 ◽  
Author(s):  
JEFFREY H. SKEVINGTON ◽  
CHRISTIAN KEHLMAIER ◽  
GUNILLA STÅHLS
Keyword(s):  
Dna Barcoding ◽  
Sequence Data ◽  
Phylogenetic Signal ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Base Pairs ◽  
Data Set ◽  
Taxonomic Decision ◽  
Morphological Species

Sequence data from 658 base pairs of mitochondrial cytochrome c oxidase I (cox1) were analysed for 28 described species of Pipunculidae (Diptera) in an effort to test the concept of DNA Barcoding on this family. Two recently revised but distantly related pipunculid lineages with presumed different evolutionary histories were used for the test (Clistoabdominalis Skevington, 2001 and Nephrocerus Zetterstedt, 1838). An effort was made to test the concept using sister taxa and morphologically similar sibling species swarms in these two genera. Morphological species concepts for Clistoabdominalis taxa were either supported by cox1 data or found to be too broad. Most of the discordance could be accounted for after reassessing morphological characters. In these cases, the molecular data were invaluable in assisting taxonomic decision-making. The radiation of Nearctic species of Nephrocerus could not be diagnosed using cox1. The ability of cox1 to recover phylogenetic signal was also tested on Clistoabdominalis. Morphological data for Clistoabdominalis were combined with the molecular data set. The pipunculid phylogeny from molecular data closely resembles the published phylogeny based on morphology. Partitioned Bremer support is used to localize areas of conflict between the datasets.

Paleontological data and molecular phylogenetic analysis

Paleobiology ◽  
1994 ◽  
Vol 20 (3) ◽  
pp. 259-273 ◽  
Author(s):  
Andrew B. Smith ◽  
D. T. J. Littlewood
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Evolution ◽  
Sequence Data ◽  
Molecular Data ◽  
Total Evidence ◽  
Molecular Phylogenetic Analysis ◽  
Molecular Sequence Data ◽  
Geological Past ◽  
Molecular Phylogenetic ◽  
Rates Of Molecular Evolution

Molecular data are becoming an indispensable tool for the reconstruction of phylogenies. Fossil molecular data remain scarce, but have the potential to resolve patterns of deep branching and provide empirical tests of tree reconstruction techniques. A total evidence approach, combining and comparing complementary morphological, molecular and stratigraphical data from both recent and fossil taxa, is advocated as the most promising way forward because there are several well-established problems that can afflict the analysis of molecular sequence data sometimes resulting in spurious tree topologies. The integration of evidence allows us to: (1) choose suitable taxa for molecular phylogenetic analysis for the question at hand; (2) discriminate between conflicting hypotheses of taxonomic relationship and phylogeny; (3) evaluate procedures and assumptions underlying methods of building trees; and (4) estimate rates of molecular evolution in the geological past. Paleontology offers a set of independent data for comparison and corroboration of analyses and provides the only direct means of calibrating molecular trees, thus giving insight into rates of molecular evolution in the geological past.

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