On taxonomic membership

Paleobiology ◽  
2011 ◽  
Vol 37 (3) ◽  
pp. 519-536 ◽  
Author(s):  
Bruce H. Wilkinson
Keyword(s):  
Adaptive Radiation ◽  
Taxonomic Group ◽  
Plate Model ◽  
Model Yield ◽  
Taxonomic Groups

Taxonomic membership frequencies exhibit distributions in which groups with few numbers of subtaxa are much more common in a clade than those with more subtaxa. Here, a “broken plate” model is developed to describe such taxonomic memberships; some higher taxonomic group (the plate) is randomly subdivided into intermediate taxonomic units (plate fragments), whose sizes are dependent on the number of taxonomic subunits that they each contain. Theoretical distributions of membership frequencies produced by this model yield a superior fit to data from both modern and fossil groups, as illustrated by classifications for primarily fossil brachiopods and entirely modern mammals. The nature of these distributions is consistent with the contention that Linnaean membership frequencies result from the random partitioning of taxonomic/morphologic space. Moreover, numbers of taxa contained within hierarchically equivalent groups are unrelated, as are membership numbers at taxonomically higher and lower levels of consideration. Agreement between observed taxonomic memberships and those anticipated from the random partitioning of diversity as described by the “broken plate” model bears directly on a number of fundamental questions including the significance of extreme polytypy and inferred causes of adaptive radiation within many taxonomic groups.

scholarly journals The pitfalls of biodiversity proxies: Differences in richness patterns of birds, trees and understudied diversity across Amazonia

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Camila D. Ritter ◽  
Søren Faurby ◽  
Dominic J. Bennett ◽  
Luciano N. Naka ◽  
Hans ter Steege ◽  
...  
Keyword(s):  
Species Richness ◽  
Large Scale ◽  
Spatial Scales ◽  
Local Environment ◽  
Life Forms ◽  
Taxonomic Group ◽  
Diversity Gradients ◽  
Richness Patterns ◽  
Taxonomic Groups ◽  
Micro Organisms

AbstractMost knowledge on biodiversity derives from the study of charismatic macro-organisms, such as birds and trees. However, the diversity of micro-organisms constitutes the majority of all life forms on Earth. Here, we ask if the patterns of richness inferred for macro-organisms are similar for micro-organisms. For this, we barcoded samples of soil, litter and insects from four localities on a west-to-east transect across Amazonia. We quantified richness as Operational Taxonomic Units (OTUs) in those samples using three molecular markers. We then compared OTU richness with species richness of two relatively well-studied organism groups in Amazonia: trees and birds. We find that OTU richness shows a declining west-to-east diversity gradient that is in agreement with the species richness patterns documented here and previously for birds and trees. These results suggest that most taxonomic groups respond to the same overall diversity gradients at large spatial scales. However, our results show a different pattern of richness in relation to habitat types, suggesting that the idiosyncrasies of each taxonomic group and peculiarities of the local environment frequently override large-scale diversity gradients. Our findings caution against using the diversity distribution of one taxonomic group as an indication of patterns of richness across all groups.

DNA metabarcode choice and design

2018 ◽  
Author(s):  
Pierre Taberlet ◽  
Aurélie Bonin ◽  
Lucie Zinger ◽  
Eric Coissac
Keyword(s):  
In Silico ◽  
Taxonomic Group ◽  
Taxonomic Resolution ◽  
Software Suite ◽  
Resolution Power ◽  
Wide Range ◽  
Dna Metabarcoding ◽  
Primer Annealing ◽  
Taxonomic Groups ◽  
The Ideal

Chapter “DNA metabarcode choice and design” develops the properties of the ideal metabarcode in a given context, including conservation of the primer annealing regions and resolution power across the target taxonomic group of interest. It also highlights the experimental constraints influencing the choice of a metabarcode in practice. A detailed tutorial illustrates how to design and test metabarcoding primers in silico with the programs ecoPrimers, ecoPCR, and the software suite OBITools. Command lines and example files are provided to design and test universal metabarcoding primers for Bacteria. Chapter 2 also gives statistics about the taxonomic resolution and primer conservation of more than 60 metabarcodes available for DNA metabarcoding analysis of a wide range of taxonomic groups.

What We Do and Don’t Know

2016 ◽  
Author(s):  
Andrew P. Hendry
Keyword(s):  
Evolutionary Dynamics ◽  
Theoretical Models ◽  
Taxonomic Group ◽  
Laboratory Studies ◽  
Darwin's Finches ◽  
Darwin’S Finches ◽  
Taxonomic Groups ◽  
The Relationship

This chapter describes the scope and limitation of what people know about eco-evolutionary dynamics. What they are striving to explain is the relationship between ecology and evolution, seeking to elucidate these relationships for a specific taxonomic group in a specific environment, such as Darwin's finches in Galapagos. In such cases, scholars need detailed studies of that particular group in that particular environment, ideally supplemented with theoretical models and laboratory studies that help to elucidate mechanisms. Alternatively, one might seek to discover generalities of relationships between ecology and evolution that transcend specific groups and environments. Ultimately, the chapter argues that no matter the goal, scholars need detailed studies of specific taxonomic groups in specific environments.

DNA homology, phage-typing, and cross-nodulation studies of rhizobia infecting Galega species

1983 ◽  
Vol 29 (7) ◽  
pp. 781-789 ◽  
Author(s):  
Krishna Lindström ◽  
B. D. W. Jarvis ◽  
P. E. Lindström ◽  
J. J. Patel
Keyword(s):  
Host Plants ◽  
Taxonomic Status ◽  
Phage Typing ◽  
Taxonomic Group ◽  
Dna Homology ◽  
Fast Growing ◽  
The Mean ◽  
Taxonomic Groups

The taxonomic status of Rhizobium nodulating Galega sp. is poorly defined. Earlier reports suggest that the rhizobia infecting G. officinalis should be included in the R. leguminosarum species or in the "fast-growing lupin – cowpea complex." Therefore organisms nodulating G. orientalis and G. officinalis were studied using cross nodulation, DNA homology, and phage typing. No cross-nodulation relationship between the Galega rhizobia and rhizobial strains from the major taxonomic groups was found. The mean relative DNA homology of 10 strains of Rhizobium nodulating Galega with reference DNA from strain HAMBI 540, which forms effective nodules on G. orientalis, was 77 ± 9%, compared with 19 ± 6% for 20 strains from other host plants. The Galega rhizobia formed a unique phage-typing group, not related to the major groups of fast growers, in agreement with the DNA homology and cross-nodulation results. These data indicate that the Galega rhizobia form a specific taxonomic group within the genus Rhizobium.

scholarly journals Thailandina and Neothailandina and their family Thailandinidae salvaged: a valid taxonomic group of peculiar Permian fusuline Foraminifera

2021 ◽  
pp. 1-6
Author(s):  
Katsumi Ueno
Keyword(s):  
Middle Permian ◽  
Taxonomic Group ◽  
New Genera ◽  
Taxonomic Note ◽  
Taxonomic Groups ◽  
Central Thailand

The fusuline genera Thailandina Toriyama and Kanmera, 1968 and Neothailandina Toriyama and Kanmera, 1968 were established by Toriyama and Kanmera (1968) based on material from the Khao Phlong Phrab section of the Permian Rat Buri Limestone in central Thailand that is currently assigned to the Khao Khad Formation of the Saraburi Group (Ueno and Charoentitirat, 2011). These fusuline genera are peculiar in having parachomata and replaced tests by secondary mineralization. Moreover, Neothailandina was described to have a test with transverse septula, considered to be characteristic for Neoschwagerinidae. Based on these remarkable test features, Toriyama and Kanmera (1968) newly introduced the subfamily Thailandininae to accommodate these two new genera and assigned it to the Neoschwagerinidae, despite the lack of septula in Thailandina. Later, Kobayashi et al. (2010) argued that Thailandina and Neothailandina are just a mixed grouping of several known genera of schwagerinids, verbeekinids, and neoschwagerinids that are too altered by recrystallization to be recognizable, and rejected the taxonomic validity of these two genera as well as Thailandininae. The Khao Phlong Phrab section represents one of the standard late Cisuralian−Guadalupian (late early−middle Permian) fusuline successions in the eastern Paleotethys (Zhang and Wang, 2018) and contains not only Thailandina and Neothailandina but also abundant schwagerinid, verbeekinid, and neoschwagerinid fusulines (Toriyama, 1975; Fig. 1). I investigated the original specimens described by Toriyama and Kanmera (1968) and Toriyama (1975) from the section that are housed in the Department of Earth and Planetary Sciences of Kyushu University, Japan. I found that most of the grounds for Kobayashi et al.'s (2010) arguments to regard the thailandinin genera as taxonomically invalid are not supported by observations on these specimens as explained in the account that follows. In this taxonomic note, I propose that Thailandina and Neothailandina, and their family Thailandinidae, should be retained as valid taxonomic groups.

scholarly journals Time lags in reporting of biological invasions: the case of Mediterranean Sea

2019 ◽  
Vol 20 (2) ◽  
pp. 469 ◽  
Author(s):  
ARGYRO ZENETOS ◽  
EIRINI GRATSIA ◽  
ANA-CRISTINA CARDOSO ◽  
KONSTANTINOS TSIAMIS
Keyword(s):  
Biological Invasions ◽  
Mediterranean Sea ◽  
Time Lag ◽  
Taxonomic Group ◽  
Time Lags ◽  
Indigenous Species ◽  
Prevention Measures ◽  
The Mediterranean ◽  
Taxonomic Groups ◽  
Non Indigenous Species

Time lags in non-indigenous species (NIS) reporting can create uncertainty in the analysis of NIS introduction rates, which can lead to inadequate actions, prevention measures and their evaluation. The present study aims to highlight time lags in marine NIS reporting in the Mediterranean Sea, i.e.: the time that mediates from the detection of a new NIS in the Mediterranean Sea until its publication. Our results revealed that the time lag in NIS reporting in the Mediterranean Sea has been considerably decreased during the last decades. There is also a noticeable difference in the time lag of reporting NIS in association with the taxonomic group of the species. Fish have generally shorter time lags in their reporting when compared with other taxonomic groups (e.g. macrophytes, Annelida, Bryozoa). Considering the widespread concern on marine introductions, it is essential to recognize the importance of taking into account time lags of reporting NIS that skew introduction patterns of marine NIS, permitting thus more accurate management assessments.

New species of Nematothallus from the Silurian Bloomsburg Formation of Pennsylvania

1988 ◽  
Vol 62 (6) ◽  
pp. 967-982 ◽  
Author(s):  
Paul K. Strother
Keyword(s):  
New Species ◽  
Adaptive Radiation ◽  
Fossil Record ◽  
Habitat Characteristics ◽  
Taxonomic Group ◽  
Terrestrial Plant ◽  
Plant Kingdom ◽  
Three New Species

The early terrestrial fossil record contains numerous Siluro-Devonian problematic Thallophyta which have morphological and habitat characteristics intermediate between the algae and the embryophytic plant kingdom. Three new species of the genus Nematothallus Lang (N. taenia, N. lobata, and N. elliptica) are described from a coaly lens in the Bloomsburg Formation (Ludlow). They are included in the order Nematophytales, which is placed in a new informal taxonomic group, Paraphyta, intended to include enigmatic, terrestrial plant-like fossils. These species designations are based upon the gross morphology of carbonized thalli which consist of an underlying anatomy of flattened tubular elements. The association and attachment of cuticles and axes of ?Prototaxites to Nematothallus is clearly demonstrated in these collections. The morphological and anatomical variety expressed in the numerous fragments of thalli from the deposit implies moderate levels of organic diversity in a “flora” of nonvascular, terrestrial plant-like thallophytes which predates the adaptive radiation of the embryophytes.

scholarly journals A systematic survey of regional multitaxon biodiversity: evaluating strategies and coverage

2017 ◽  
Author(s):  
Ane Kirstine Brunbjerg ◽  
Hans Henrik Bruun ◽  
Lars Brøndum ◽  
Aimée T. Classen ◽  
Lars Dalby ◽  
...  
Keyword(s):  
Species Richness ◽  
Plant Species ◽  
Environmental Gradients ◽  
Vascular Plant ◽  
Taxonomic Group ◽  
Spatial And Temporal Variation ◽  
Soil Dna ◽  
Wide Range ◽  
Study Sites ◽  
Taxonomic Groups

AbstractBackgroundIn light of the biodiversity crisis and our limited ability to explain variation in biodiversity, tools to quantify spatial and temporal variation in biodiversity and its underlying drivers are critically needed. Inspired by the recently published ecospace framework, we developed and tested a sampling design for environmental and biotic mapping. We selected 130 study sites (40 × 40 m) across Denmark using stratified random sampling along the major environmental gradients underlying biotic variation. Using standardized methods, we collected site species data on vascular plants, bryophytes, macrofungi, lichens, gastropods and arthropods. To evaluate sampling efficiency, we calculated regional coverage (relative to the known species number per taxonomic group), and site scale coverage (i.e., sample completeness per taxonomic group at each site). To extend taxonomic coverage to organisms that are difficult to sample by classical inventories (e.g., nematodes and non-fruiting fungi), we collected soil for metabarcoding. Finally, to assess site conditions, we mapped abiotic conditions, biotic resources and habitat continuity.ResultsDespite the 130 study sites only covering a minute fraction (0.0005 %) of the total Danish terrestrial area, we found 1774 species of macrofungi (54 % of the Danish fungal species pool), 663 vascular plant species (42 %), 254 bryophyte species (41 %) and 200 lichen species (19 %). For arthropods, we observed 330 spider species (58 %), 123 carabid beetle species (37 %) and 99 hoverfly species (33 %). Correlations among species richness for taxonomic groups were predominantly positive. Overall, sample coverage was remarkably high across taxonomic groups and sufficient to capture substantial spatial variation in biodiversity across Denmark. This inventory is nationally unprecedented in detail and resulted in the discovery of 143 species with no previous record for Denmark. Comparison between plant OTUs detected in soil DNA and observed plant species confirmed the usefulness of carefully curated environmental DNA-data. Species richness did not correlate well among taxa suggesting differential and complex biotic responses to environmental variation.ConclusionsWe successfully and adequately sampled a wide range of diverse taxa along key environmental gradients across Denmark using an approach that includes multi-taxon biodiversity assessment and ecospace mapping. Our approach is applicable to assessments of biodiversity in other regions and biomes where species are structured along environmental gradient.

scholarly journals A systematic survey of regional multi-taxon biodiversity: evaluating strategies and coverage

BMC Ecology ◽  
2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Ane Kirstine Brunbjerg ◽  
Hans Henrik Bruun ◽  
Lars Brøndum ◽  
Aimée T. Classen ◽  
Lars Dalby ◽  
...  
Keyword(s):  
Plant Species ◽  
Environmental Gradients ◽  
Vascular Plant ◽  
Taxonomic Group ◽  
Spatial And Temporal Variation ◽  
Species Number ◽  
Soil Dna ◽  
Wide Range ◽  
Study Sites ◽  
Taxonomic Groups

Abstract Background In light of the biodiversity crisis and our limited ability to explain variation in biodiversity, tools to quantify spatial and temporal variation in biodiversity and its underlying drivers are critically needed. Inspired by the recently published ecospace framework, we developed and tested a sampling design for environmental and biotic mapping. We selected 130 study sites (40 × 40 m) across Denmark using stratified random sampling along the major environmental gradients underlying biotic variation. Using standardized methods, we collected site species data on vascular plants, bryophytes, macrofungi, lichens, gastropods and arthropods. To evaluate sampling efficiency, we calculated regional coverage (relative to the known species number per taxonomic group), and site scale coverage (i.e., sample completeness per taxonomic group at each site). To extend taxonomic coverage to organisms that are difficult to sample by classical inventories (e.g., nematodes and non-fruiting fungi), we collected soil for metabarcoding. Finally, to assess site conditions, we mapped abiotic conditions, biotic resources and habitat continuity. Results Despite the 130 study sites only covering a minute fraction (0.0005%) of the total Danish terrestrial area, we found 1774 species of macrofungi (54% of the Danish fungal species pool), 663 vascular plant species (42%), 254 bryophyte species (41%) and 200 lichen species (19%). For arthropods, we observed 330 spider species (58%), 123 carabid beetle species (37%) and 99 hoverfly species (33%). Overall, sample coverage was remarkably high across taxonomic groups and sufficient to capture substantial spatial variation in biodiversity across Denmark. This inventory is nationally unprecedented in detail and resulted in the discovery of 143 species with no previous record for Denmark. Comparison between plant OTUs detected in soil DNA and observed plant species confirmed the usefulness of carefully curated environmental DNA-data. Correlations among species richness for taxonomic groups were predominantly positive, but did not correlate well among all taxa suggesting differential and complex biotic responses to environmental variation. Conclusions We successfully and adequately sampled a wide range of diverse taxa along key environmental gradients across Denmark using an approach that includes multi-taxon biodiversity assessment and ecospace mapping. Our approach is applicable to assessments of biodiversity in other regions and biomes where species are structured along environmental gradient.

scholarly journals Changes in body size spectra of benthic caridean shrimps (Decapoda: Caridea) and snails (Gastropoda) as response to seasonal variability

2016 ◽  
Vol 64 (1) ◽  
pp. 33
Author(s):  
Ernesto Iván Badano ◽  
Fabio A. Labra ◽  
Cecilia G. Martínez-Pérez ◽  
Carlos H. Vergara
Keyword(s):  
Body Size ◽  
Environmental Changes ◽  
Spatial Scales ◽  
Taxonomic Group ◽  
Eastern Coast ◽  
Power Scaling ◽  
Regression Analyses ◽  
Size Spectra ◽  
Taxonomic Groups ◽  
The Impact

Ecologists have been largely interested in the description and understanding of the power scaling relationships between body size and abundance of organisms. Many studies have focused on estimating the exponents of these functions across taxonomic groups and spatial scales, to draw inferences about the processes underlying this pattern. The exponents of these functions usually approximate -3/4 at geographical scales, but they deviate from this value when smaller spatial extensions are considered. This has led to propose that body size-abundance relationships at small spatial scales may reflect the impact of environmental changes. This study tests this hypothesis by examining body size spectra of benthic shrimps (Decapoda: Caridea) and snails (Gastropoda) in the Tamiahua lagoon, a brackish body water located in the Eastern coast of Mexico. We measured water quality parameters (dissolved oxygen, salinity, pH, water temperature, sediment organic matter and chemical oxygen demand) and sampled benthic macrofauna during three different climatic conditions of the year (cold, dry and rainy season). Given the small size of most individuals in the benthic macrofaunal samples, we used body volume, instead of weight, to estimate their body size. Body size-abundance relationships of both taxonomic groups were described by tabulating data from each season into base-2 logarithmic body size bins. In both taxonomic groups, observed frequencies per body size class in each season were standardized to yield densities (i.e., individuals/m3). Nonlinear regression analyses were separately performed for each taxonomic group at each season to assess whether body size spectra followed power scaling functions. Additionally, for each taxonomic group, multiple regression analyses were used to determine whether these relationships varied among seasons. Our results indicated that, while body size-abundance relationships in both taxonomic groups followed power functions, the parameters defining the shape of these relationships varied among seasons. These variations in the parameters of the body size-abundance relationships seems to be related to changes in the abundance of individuals within the different body size classes, which seems to follow the seasonal changes that occur in the environmental conditions of the lagoon. Thus, we propose that these body size-abundance relationships are influenced by the frequency and intensity of environmental changes affecting this ecosystem.

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