Augmentation of French grunt diet description using combined visual and DNA-based analyses

2012 ◽  
Vol 63 (8) ◽  
pp. 740 ◽  
Author(s):  
John S. Hargrove ◽  
Daryl C. Parkyn ◽  
Debra J. Murie ◽  
Amanda W. J. Demopoulos ◽  
James D. Austin
Keyword(s):  
Visual Analysis ◽  
Stomach Contents ◽  
Molecular Data ◽  
Dietary Analysis ◽  
Haemulon Flavolineatum ◽  
The Family ◽  
Pharyngeal Teeth ◽  
Family Level ◽  
Trophic Linkages ◽  
French Grunt

Trophic linkages within a coral-reef ecosystem may be difficult to discern in fish species that reside on, but do not forage on, coral reefs. Furthermore, dietary analysis of fish can be difficult in situations where prey is thoroughly macerated, resulting in many visually unrecognisable food items. The present study examined whether the inclusion of a DNA-based method could improve the identification of prey consumed by French grunt, Haemulon flavolineatum, a reef fish that possesses pharyngeal teeth and forages on soft-bodied prey items. Visual analysis indicated that crustaceans were most abundant numerically (38.9%), followed by sipunculans (31.0%) and polychaete worms (5.2%), with a substantial number of unidentified prey (12.7%). For the subset of prey with both visual and molecular data, there was a marked reduction in the number of unidentified sipunculans (visual – 31.1%, combined – 4.4%), unidentified crustaceans (visual – 15.6%, combined – 6.7%), and unidentified taxa (visual – 11.1%, combined – 0.0%). Utilising results from both methodologies resulted in an increased number of prey placed at the family level (visual – 6, combined – 33) and species level (visual – 0, combined – 4). Although more costly than visual analysis alone, our study demonstrated the feasibility of DNA-based identification of visually unidentifiable prey in the stomach contents of fish.

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 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.

scholarly journals Diversity of ants and mites in the diet of the Brazilian frog Chiasmocleis leucosticta (Anura: Microhylidae)

2017 ◽  
Vol 17 (3) ◽  
Author(s):  
Mariana S. Lopes ◽  
Ricardo S. Bovendorp ◽  
Gilberto José de Moraes ◽  
Alexandre Reis Percequillo ◽  
Jaime Bertoluci
Keyword(s):  
Diet Composition ◽  
Statistical Difference ◽  
Stomach Contents ◽  
Southeastern Brazil ◽  
Pitfall Traps ◽  
Prey Category ◽  
Food Items ◽  
The Family ◽  
Family Level ◽  
Males And Females

Abstract We describe here the diet of the microhylid frog Chiasmocleis leucosticta based on the stomach contents of 72 individuals (47 males and 25 females) collected in pitfall traps at the Reserva Florestal de Morro Grande, state of São Paulo, southeastern Brazil. We identified 1,981 food items distributed in 13 prey categories of arthropods, mainly ants, mites and collembolans. Formicidae was the most abundant and frequent prey category, including 16 genera from seven subfamilies, and data on ant availability in the habitat suggest that C. leucosticta selects ants actively. The second main prey category was Acari, predominantly represented by mites of the suborder Oribatida. This is the first work identifying mites to the family level in the diet of a Microhylidae. There was no statistical difference between males and females regarding diet composition.

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 New family-level characters for Platygastroidea

2021 ◽  
Vol 87 ◽  
pp. 235-249
Author(s):  
István Mikó ◽  
Monique Raymond ◽  
Elijah J. Talamas
Keyword(s):  
Fore Wing ◽  
Molecular Data ◽  
Parasitoid Wasps ◽  
Anterior Portion ◽  
New Family ◽  
Internal Morphology ◽  
Phylogenetic Implications ◽  
The Family ◽  
Family Level

Platygastridae (Hymenoptera) is a diverse family of parasitoid wasps for which few studies of internal morphology have been conducted. The monophyly of the group is undisputed based on recently published molecular data, but based on morphology, the family is diagnosable from other platygastroids only by a combination of character reductions. In the present study we explored the mesosoma of Platygastroidea and found two new synapomorphies for Platygastridae: an externally visible anterior mesofurcal pit, which corresponds to an invagination that connects to the anterior portion of the mesofurca, and internally, a posteriorly shifted origin of the first wing flexors. The absence of a mesofurcal bridge and the exclusively mesopectal origin of the fore wing flexors are treated as synapomorphies for Platygastridae+Janzenellidae. Phylogenetic implications and evolutionary hypotheses regarding these traits are discussed.

scholarly journals Designation of a new family group name, Tonzidae fam. nov., for the genus Tonza (Lepidoptera, Yponomeutoidea), based on immature stages of Tonza citrorrhoa

2018 ◽  
Author(s):  
Shigeki Kobayashi ◽  
Haruka Matsuoka ◽  
Masaaki Kimura ◽  
Jae-Cheon Sohn ◽  
Yutaka Yoshiyasu ◽  
...  
Keyword(s):  
Dna Barcode ◽  
Molecular Data ◽  
Systematic Position ◽  
Family Group ◽  
Immature Stages ◽  
Dna Barcodes ◽  
New Family ◽  
The Family ◽  
Family Level ◽  
First Time

The systematic position of Tonza Walker, 1864 is re-evaluated, based on the characteristics of immature stages and DNA barcodes. Larvae and pupae of Tonza citrorrhoa Meyrick, 1905 are described and illustrated for the first time. Larvae of this species form a loose web among the leaves and branches of the host plant, Putranjiva matsumurae Koidz. (Putranjivaceae Endl.). The immature stages of Tonza exhibit four unique apomorphies including: in the larva, the prolegs on A5 and A6 absent, and the seta L2 on the A1–A8 very small; in the pupa, four minute knobs are positioned in the middle portion on abdominal segments V and VI; while its caudal processes possess a W-shaped spine with numerous minute spines. These characteristics clearly distinguish Tonza from other yponomeutoid families and hence, we propose a new family group name, Tonzidae Kobayashi & Sohn fam. nov., for the genus Tonza. Existing DNA barcode data suggest a relationship with Glyphipterigidae Stainton, 1854. The family level status of Tonzidae fam. nov. provides a hypothesis that needs to be tested with larger molecular data.

scholarly journals Acari of Canada

ZooKeys ◽  
2019 ◽  
Vol 819 ◽  
pp. 77-168 ◽  
Author(s):  
Frédéric Beaulieu ◽  
Wayne Knee ◽  
Victoria Nowell ◽  
Marla Schwarzfeld ◽  
Zoë Lindo ◽  
...  
Keyword(s):  
New Records ◽  
Molecular Data ◽  
Actual Number ◽  
Aquatic Habitats ◽  
Feather Mites ◽  
Index Numbers ◽  
The Family ◽  
Family Level ◽  
The Usa ◽  
Substantial Progress

Summaries of taxonomic knowledge are provided for all acarine groups in Canada, accompanied by references to relevant publications, changes in classification at the family level since 1979, and notes on biology relevant to estimating their diversity. Nearly 3000 described species from 269 families are recorded in the country, representing a 56% increase from the 1917 species reported by Lindquist et al. (1979). An additional 42 families are known from Canada only from material identified to family- or genus-level. Of the total 311 families known in Canada, 69 are newly recorded since 1979, excluding apparent new records due solely to classification changes. This substantial progress is most evident in Oribatida and Hydrachnidia, for which many regional checklists and family-level revisions have been published. Except for recent taxonomic leaps in a few other groups, particularly of symbiotic mites (Astigmata: feather mites; Mesostigmata: Rhinonyssidae), knowledge remains limited for most other taxa, for which most species records are unpublished and may require verification. Taxonomic revisions are greatly needed for a large majority of families in Canada. Based in part on species recorded in adjacent areas of the USA and on hosts known to be present here, we conservatively estimate that nearly 10,000 species of mites occur in Canada, but the actual number could be 15,000 or more. This means that at least 70% of Canada’s mite fauna is yet unrecorded. Much work also remains to match existing molecular data with species names, as less than 10% of the ~7500 Barcode Index Numbers for Canadian mites in the Barcode of Life Database are associated with named species. Understudied hosts and terrestrial and aquatic habitats require investigation across Canada to uncover new species and to clarify geographic and ecological distributions of known species.

Five new morphological types of virgulate and microcotylous xiphidiocercariae based on morphological and molecular phylogenetic analyses

2019 ◽  
Vol 94 ◽  
Author(s):  
S.V. Shchenkov ◽  
S.A. Denisova ◽  
G.A. Kremnev ◽  
A.A. Dobrovolskij
Keyword(s):  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
The Family ◽  
Family Level ◽  
Molecular Phylogenetic ◽  
Morphological And Molecular Data ◽  
First Time

Abstract The phylogenetic position of most xiphidiocercariae from subgroups Cercariae virgulae and Cercariae microcotylae remains unknown or unclear, even at the family level. In this paper, we studied the morphology and molecular phylogeny of 15 microcotylous and virgulate cercariae (11 new and four previously described ones). Based on morphological and molecular data, we suggested five distinct morphological types of xiphidiocercariae, which are a practical alternative to Cercariae virgulae and Cercariae microcotylae subgroups. Four of these types correspond to actual digenean taxa (Microphallidae, Lecithodendriidae, Pleurogenidae and Prosthogonimidae), while the fifth is represented by Cercaria nigrospora Wergun, 1957, which we classified on the basis of molecular data for the first time. We reassessed the relative importance of morphological characters used for the classification of virgulate and microcotylous cercariae, and discussed the main evolutionary trends within xiphidiocercariae. Now stylet cercariae can be reliably placed into several sub-taxa of Microphalloidea on the basis of their morphological features.

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.

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