scholarly journals Completeness metrics and the quality of the sauropodomorph fossil record through geological and historical time

Paleobiology ◽  
2010 ◽  
Vol 36 (2) ◽  
pp. 283-302 ◽  
Author(s):  
Philip D. Mannion ◽  
Paul Upchurch
Keyword(s):  
Sea Level ◽  
Fossil Record ◽  
Quantitative Methods ◽  
Phylogenetic Analyses ◽  
Type Specimen ◽  
Time Interval ◽  
Historical Time ◽  
Rock Outcrop ◽  
Type Specimens ◽  
Fossil Remains

Despite increasing concerns about the effect of sampling biases on our reading of the fossil record, few studies have considered the completeness of the fossil remains themselves, and those that have tend to apply non-quantitative measures of preservation quality. Here we outline two new types of metric for quantifying the completeness of the fossil remains of taxa through time, using sauropodomorph dinosaurs as a case study. The “Skeletal Completeness Metric” divides the skeleton up into percentages based on the amount of bone for each region, whereas the “Character Completeness Metric” is based on the number of characters that can be scored for each skeletal element in phylogenetic analyses. For both metrics we calculated the completeness of the most complete individual and of the type specimen. We also calculated how well the taxon as a whole is known from its remains. We then plotted these results against both geological and historical time, and compared curves of the former with fluctuations in sauropodomorph diversity, sea level, and sedimentary rock outcrop area. Completeness through the Mesozoic shows a number of peaks and troughs; the Early Jurassic (Hettangian–Sinemurian) is the interval with highest completeness, whereas the mid-to-Late Cretaceous has completeness levels that are consistently lower than the rest of the Mesozoic. Completeness shows no relationship to rock outcrop area, but it is negatively correlated with sea level during the Jurassic–Early Cretaceous and correlated with diversity in the Cretaceous. Completeness of sauropodomorph type specimens has improved from 1830 to the present, supporting the conclusions of other recent studies. However, when this time interval is partitioned, we find no trend for an increase in completeness from the 1990s onward. Moreover, the 2000s represent one of the poorest decades in terms of average type specimen completeness. These results highlight the need for quantitative methods when assessing fossil record quality through geological time or when drawing conclusions about historical trends in the completeness of taxa. The new metrics may also prove useful as sampling proxies in diversity studies.

Maluti Mystery: A systematic review of Amietia vertebralis (Hewitt, 1927) and Strongylopus hymenopus (Boulenger, 1920) (Anura: Pyxicephalidae)

Zootaxa ◽  
2008 ◽  
Vol 1962 (1) ◽  
pp. 33-48 ◽  
Author(s):  
JEANNE TARRANT ◽  
MICHAEL J. CUNNINGHAM ◽  
LOUIS H. DU PREEZ
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Original Description ◽  
Type Specimen ◽  
Systematic Position ◽  
Type Specimens ◽  
Morphological Examination ◽  
Species Type ◽  
Original Application

The taxonomic status of Amietia vertebralis and Strongylopus hymenopus, two frogs restricted to the Maluti-Drakensberg highlands in southern Africa, is unclear. Here, morphological examination and phylogenetic analyses elucidate the systematic position of these two species. Type specimens of both species were examined and compared with more recent collections to clarify their identity. These comparisons revealed discrepancies between the original application of these names and their current usage. The holotype and original description of A. vertebralis match specimens from an extant population at that species’ type locality that are currently assigned to S. hymenopus. Furthermore, the type specimen of S. hymenopus is of uncertain provenance and does not match well with either of the forms currently associated with these names. We assessed both intraspecific and interspecific variability using DNA sequence data. Broad sampling of the form currently assigned to A. vertebralis revealed very little genetic variation thereby dispelling the hypothesis that this is a compound taxon. The generic placement of both species within the family Pyxicephalidae was resolved using a combined dataset of mitochondrial 16S rDNA and nuclear RAG1 gene sequences. The form currently recognised as S. hymenopus was excluded from the otherwise monophyletic genus Strongylopus, and was placed instead within Amietia. Based on these data a revised application of both species names is recommended here. Populations currently assigned to Amietia vertebralis are referred to Amietia umbraculata and those attributed to Strongylopus hymenopus are referred instead to Amietia vertebralis.

scholarly journals Multiple cenozoic invasions of Africa by penguins (Aves, Sphenisciformes)

2011 ◽  
Vol 279 (1730) ◽  
pp. 1027-1032 ◽  
Author(s):  
Daniel T. Ksepka ◽  
Daniel B. Thomas
Keyword(s):  
Sea Level ◽  
Fossil Record ◽  
Phylogenetic Analyses ◽  
Late Cenozoic ◽  
Early Pliocene ◽  
Fossil Material ◽  
Spheniscus Demersus ◽  
Regional Sea Level ◽  
African Penguin ◽  
Penguin Species

Africa hosts a single breeding species of penguin today, yet the fossil record indicates that a diverse array of now-extinct taxa once inhabited southern African coastlines. Here, we show that the African penguin fauna had a complex history involving multiple dispersals and extinctions. Phylogenetic analyses and biogeographic reconstructions incorporating new fossil material indicate that, contrary to previous hypotheses, the four Early Pliocene African penguin species do not represent an endemic radiation or direct ancestors of the living Spheniscus demersus (blackfooted penguin). A minimum of three dispersals to Africa, probably assisted by the eastward-flowing Antarctic Circumpolar and South Atlantic currents, occurred during the Late Cenozoic. As regional sea-level fall eliminated islands and reduced offshore breeding areas during the Pliocene, all but one penguin lineage ended in extinction, resulting in today's depleted fauna.

Ellipsomyxa ariusi sp. nov. (Myxosporea: Ceratomyxidae), a new myxosporean infecting the gallbladder of threadfin sea catfish Arius arius in India

2020 ◽  
Vol 142 ◽  
pp. 83-97
Author(s):  
A Chandran ◽  
PU Zacharia ◽  
TV Sathianandan ◽  
NK Sanil
Keyword(s):  
Phylogenetic Analyses ◽  
Type Specimen ◽  
Ssu Rdna ◽  
Fish Host ◽  
Present Species ◽  
Epithelial Layer ◽  
Histopathological Changes ◽  
Mucus Production ◽  
High Bootstrap ◽  
A New Species

The present study describes a new species of myxosporean, Ellipsomyxa ariusi sp. nov., infecting the gallbladder of the threadfin sea catfish Arius arius (Hamilton, 1822). E. ariusi sp. nov. is characterized by bivalvular, ellipsoid or elongate-oval myxospores with smooth spore valves and a straight suture, arranged at an angle to the longitudinal spore axis. Mature myxospores measured 10.1 ± 0.8 µm in length, 6.8 ± 0.5 µm in width and 7.7 ± 0.7 µm in thickness. Polar capsules are equal in size and oval to pyriform in shape. They are positioned at an angle to the longitudinal myxospore axis and open in opposite directions. Polar capsules measured 2.8 ± 0.3 µm in length and 2.5 ± 0.4 µm in width; polar filaments formed 4-5 coils, and extended to 32.2 ± 2.1 µm in length. Monosporic and disporic plasmodial stages attached to the wall of gallbladder. Molecular analysis of the type specimen generated a 1703 bp partial SSU rDNA sequence (MN892546), which was identical to the isolates from 3 other locations. In phylogenetic analyses, genus Ellipsomyxa appeared monophyletic and E. ariusi sp. nov. occupied an independent position in maximum likelihood and Bayesian inference trees with high bootstrap values. The overall prevalence of infection was 54.8% and multiway ANOVA revealed that it varied significantly with location, year, season, sex and size of the fish host. Histopathological changes associated with E. ariusi sp. nov. infection included swelling, vacuolation and detachment of epithelial layer, reduced mucus production and altered consistency and colour of bile. Based on the morphologic, morphometric and molecular differences with known species of Ellipsomyxa, and considering differences in host and geographic locations, the present species is treated as new and the name Ellipsomyxa ariusi sp. nov. is proposed.

scholarly journals Taxonomic Re-Examination of Nine Rosellinia Types (Ascomycota, Xylariales) Stored in the Saccardo Mycological Collection

2021 ◽  
Vol 9 (3) ◽  
pp. 666
Author(s):  
Niccolò Forin ◽  
Alfredo Vizzini ◽  
Federico Fainelli ◽  
Enrico Ercole ◽  
Barbara Baldan
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Illumina Miseq ◽  
Botanical Garden ◽  
Molecular Study ◽  
Its2 Sequence ◽  
Type Specimens ◽  
Its1 Sequence ◽  
Dna Sequence Data ◽  
Nomen Novum

In a recent monograph on the genus Rosellinia, type specimens worldwide were revised and re-classified using a morphological approach. Among them, some came from Pier Andrea Saccardo’s fungarium stored in the Herbarium of the Padova Botanical Garden. In this work, we taxonomically re-examine via a morphological and molecular approach nine different Roselliniasensu Saccardo types. ITS1 and/or ITS2 sequences were successfully obtained applying Illumina MiSeq technology and phylogenetic analyses were carried out in order to elucidate their current taxonomic position. Only the ITS1 sequence was recovered for Rosellinia areolata, while for R. geophila, only the ITS2 sequence was recovered. We proposed here new combinations for Rosellinia chordicola, R. geophila and R. horridula, while for R. ambigua, R. areolata, R. australis, R. romana and R. somala, we did not suggest taxonomic changes compared to the current ones. The name Rosellinia subsimilis Sacc. is invalid, as it is a later homonym of R. subsimilis P. Karst. & Starbäck. Therefore, we introduced Coniochaeta dakotensis as a nomen novum for R. subsimilis Sacc. This is the first time that these types have been subjected to a molecular study. Our results demonstrate that old types are an important source of DNA sequence data for taxonomic re-examinations.

scholarly journals A non-destructive virtual dissection by micro-CT reveals diagnostic characters in the type specimen of Caloptilia stigmatella (Lepidoptera: Gracillariidae)

Zootaxa ◽  
2018 ◽  
Vol 4441 (1) ◽  
pp. 137
Author(s):  
JEANNE ROBINSON ◽  
JEREMY GIBSON ◽  
HELBER ADRIÁN ARÉVALO-MALDONADO ◽  
JURATE DE PRINS ◽  
JAMES WINDMILL
Keyword(s):  
Type Specimen ◽  
Morphological Characters ◽  
Wide Distribution ◽  
Wing Venation ◽  
Type Specimens ◽  
Unique Type ◽  
Species Groups ◽  
Primary Type ◽  
Taxonomic Studies ◽  
Non Destructive

Nearly a century ago, wing venation was introduced in gracillariid taxonomy as a means to diagnose closely related genera and species groups. Recent advances in non-destructive virtual micro-dissections suggest promising approaches with which to revisit the relevance of wing venation characters on historic primary type specimens. Many unique type specimens in Gracillariidae and other microlepidoptera groups preserved in museum collections are in poor condition, and over the course of history have suffered loss or damage to their abdomens. Consequently, genitalia morphology is not available for diagnoses and comparisons. In this paper we emphasize the need to include the type species and type specimens into the broader context of taxonomic studies on micro-moths in general and the family Gracillariidae in particular. The genus Caloptilia has a world-wide distribution and has been the subject of research for more than 200 years, yet the generic boundaries and groupings within the genus are still unresolved due to the lack of a reliable set of taxonomic characters obtained from the primary types. We describe a method of virtual descaling of the fore- and hindwings using the unset micro-moth type specimen of Caloptilia stigmatella Fabricius, 1781, in order to demonstrate that the study of historic and fragile type specimens and diagnoses of their internal morphological characters becomes possible by applying new and non-destructive technology. 

Clathrosporium retortum, a novel aeroaquatic fungus in the Sordariomycetidae (Ascomycota) from Brazil

Phytotaxa ◽  
2015 ◽  
Vol 239 (1) ◽  
pp. 17
Author(s):  
Larissa Bernardino Moro ◽  
Gregorio Delgado ◽  
Iracema Helena SCHOENLEIN-CRUSIUS
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Type Specimen ◽  
Molecular Data ◽  
Sao Paulo ◽  
São Paulo ◽  
Present Fungus ◽  
Broad Concept ◽  
Morphological And Molecular Data ◽  
First Time

Clathrosporium retortum sp. nov., collected on submerged mixed leaf litter samples at Ilha do Cardoso State Park, São Paulo state, Brazil, is described based on morphological and molecular data. The fungus is characterized by forming whitish, dense, subglobose to irregular propagules, hyaline to subhyaline when young, subhyaline to dark brown at maturity, that are formed by densely interwoven conidial filaments with each conidial cell repeatedly branching bilaterally or occasionally unilaterally. Phylogenetic analyses using partial LSU nrDNA sequence data suggest that C. retortum belongs in the Sordariomycetes (Ascomycota) where it forms a well-supported clade with Clohesia corticola in the Sordariomycetidae, but its ordinal or familial placement remains unresolved. Its phylogenetic placement confirms the polyphyletic nature of aeroaquatic fungi like Clathrosporium, as it was distantly related to one available sequence in GenBank named as C. intricatum, the type species, which is phylogenetically related to the Helotiales (Leotiomycetes). However, due to lack of authenticity of the identity of this sequence with the type specimen of C. intricatum, a broad concept of Clathrosporium is tentatively adopted here to accommodate the present fungus instead of introducing a new genus. Beverwykella clathrata, Helicoön septatissimum and Peyronelina glomerulata are recorded for the first time from Brazil. Cancellidium applanatum and Candelabrum brocchiatum are new records for the state of São Paulo.

scholarly journals Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data

2016 ◽  
Vol 371 (1691) ◽  
pp. 20150225 ◽  
Author(s):  
Daniele Silvestro ◽  
Alexander Zizka ◽  
Christine D. Bacon ◽  
Borja Cascales-Miñana ◽  
Nicolas Salamin ◽  
...  
Keyword(s):  
North America ◽  
Fossil Record ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Historical Biogeography ◽  
Extinction Rates ◽  
Climatic Cooling ◽  
Fossil Data ◽  
Incomplete Sampling ◽  
Des Model

Methods in historical biogeography have revolutionized our ability to infer the evolution of ancestral geographical ranges from phylogenies of extant taxa, the rates of dispersals, and biotic connectivity among areas. However, extant taxa are likely to provide limited and potentially biased information about past biogeographic processes, due to extinction, asymmetrical dispersals and variable connectivity among areas. Fossil data hold considerable information about past distribution of lineages, but suffer from largely incomplete sampling. Here we present a new dispersal–extinction–sampling (DES) model, which estimates biogeographic parameters using fossil occurrences instead of phylogenetic trees. The model estimates dispersal and extinction rates while explicitly accounting for the incompleteness of the fossil record. Rates can vary between areas and through time, thus providing the opportunity to assess complex scenarios of biogeographic evolution. We implement the DES model in a Bayesian framework and demonstrate through simulations that it can accurately infer all the relevant parameters. We demonstrate the use of our model by analysing the Cenozoic fossil record of land plants and inferring dispersal and extinction rates across Eurasia and North America. Our results show that biogeographic range evolution is not a time-homogeneous process, as assumed in most phylogenetic analyses, but varies through time and between areas. In our empirical assessment, this is shown by the striking predominance of plant dispersals from Eurasia into North America during the Eocene climatic cooling, followed by a shift in the opposite direction, and finally, a balance in biotic interchange since the middle Miocene. We conclude by discussing the potential of fossil-based analyses to test biogeographic hypotheses and improve phylogenetic methods in historical biogeography.

scholarly journals A CARBONATE RAMP EVOLUTION IN THE TRANSITION FROM THE APULIA PLATFORM TO THE IONIAN BASIN DURING EARLY TO LATE CRETACEOUS (NW GREECE)

2018 ◽  
Vol 40 (1) ◽  
pp. 53
Author(s):  
K. Getsos ◽  
F. Pomoni-Papaioannou ◽  
A. Zelilidis
Keyword(s):  
Sea Level ◽  
Late Cretaceous ◽  
Facies Analysis ◽  
Carbonate Ramp ◽  
Time Interval ◽  
Storm Wave ◽  
Lowermost Part ◽  
Storm Deposits ◽  
Homoclinal Ramp ◽  
Apulia Platform

Facies analysis of Cretaceous carbonate sequences from the external and central Ionian zone revealed a homoclinal ramp model of evolution. During Berriasian to Valanginian, the carbonate ramp was differentiated to an inner-mid and outer ramp environment, which corresponded to the external and central Ionian zone, respectively, while the main inner ramp environment is assumed that was located in the Pre-Apulian zone. The external Ionian zone (inner-mid ramp) is characterized by muds tones-wackes tones with fragmented echinoderms, bivalves, radiolarians and rare aptychus considered to be deposited below the fairweather wave base (FWWB). Locally, thin graded storm deposits intervene, indicating deposition above the storm weather wave base (SWB). Minor occurrences of packs tonesgrainstones, with fragmented echinoderms, calcareous algae, tubiphytes, lagenid foraminifera and rare ooids occur, as well, considered to be deposited at the lowermost part of the inner ramp, near the constantly agitated fairweather wave base (FWWB). The central Ionian zone (outer ramp) is mainly characterized by mudstones-wackestones with abundant radiolarians and rare calpionellids and calcispheres, considered to be deposited below the storm wave base (SWB). No talus or breccias deposits were observed, during the mentioned time interval, in any part of the studied area. From Hauterivian to Turonian, continual sea-level rise, led to establishment of outer ramp environment in the external Ionian zone, over the previous inner-mid ramp, and outer ramp-basin environment, over the previous outer ramp, in the central Ionian zone. The transition from shallower to deeper conditions is characterized by an overall deposition of mudstones-wackestones with abundant radiolarians rooted in pure micrite. 

scholarly journals A new iguanodontian (Dinosauria: Ornithopoda) from the Early Cretaceous of Mongolia

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5300
Author(s):  
Terry A. Gates ◽  
Khishigjav Tsogtbaatar ◽  
Lindsay E. Zanno ◽  
Tsogtbaatar Chinzorig ◽  
Mahito Watabe
Keyword(s):  
Phylogenetic Analysis ◽  
Growth Stage ◽  
Phylogenetic Analyses ◽  
Type Specimen ◽  
Sister Taxon ◽  
New Taxon ◽  
Time Of Death ◽  
The North ◽  
Unusual Combination ◽  
Relationship Of

We describe a new iguanodontian ornithopod,Choyrodon barsboldigen. et sp. nov. from the Albian-aged Khuren Dukh Formation of Mongolia based on several partial skeletons interpreted to represent a subadult growth stage based on osteohistological features. This new taxon is diagnosed by many autapomorphies of the maxilla, nasal, lacrimal, opisthotic, predentary, and surangular.Choyrodondisplays an unusual combination of traits, possessing an open antorbital fenestra (a primitive ornithopod trait) together with derived features such as a downturned dentary and enlarged narial fenestra. Histological imaging suggests that the type specimen ofChoyrodonwould have been a subadult at the time of death. Phylogenetic analysis of two different character matrices do not positChoyrodonto be the sister taxon or to be more primitive than the iguanodontianAltirhinus kurzanovi, which is found in the same formation. The only resolved relationship of this new taxon is that it was hypothesized to be a sister-taxon with the North American speciesEolambia caroljonesa. Though discovered in the same formation andChoyrodonbeing smaller-bodied thanAltirhinus, it does not appear that the former species is an ontogimorph of the latter. Differences in morphology and results of the phylogenetic analyses support their distinction although more specimens of both species will allow better refinement of their uniqueness.

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