scholarly journals Names are not good enough: Reasoning over taxonomic change in the Andropogon complex1

Semantic Web ◽  
2016 ◽  
Vol 7 (6) ◽  
pp. 645-667 ◽  
Author(s):  
Nico M. Franz ◽  
Mingmin Chen ◽  
Parisa Kianmajd ◽  
Shizhuo Yu ◽  
Shawn Bowers ◽  
...  
Keyword(s):  
Taxonomic Change

scholarly journals Reasoning over Taxonomic Change: Exploring Alignments for the Perelleschus Use Case

PLoS ONE ◽  
2015 ◽  
Vol 10 (2) ◽  
pp. e0118247 ◽  
Author(s):  
Nico M. Franz ◽  
Mingmin Chen ◽  
Shizhuo Yu ◽  
Parisa Kianmajd ◽  
Shawn Bowers ◽  
...  
Keyword(s):  
Use Case ◽  
Taxonomic Change

A PROPOSED TAXONOMIC CHANGE IN THE TRIBE MAYDEAE (FAMILY GRAMINEAE

1942 ◽  
Vol 29 (10) ◽  
pp. 815-817 ◽  
Author(s):  
R. G. Reeves ◽  
P. C. Mangelsdorf
Keyword(s):  
Taxonomic Change

scholarly journals The reality of taxonomic change

2005 ◽  
Vol 20 (6) ◽  
pp. 278-280 ◽  
Author(s):  
P AGAPOW ◽  
R SLUYS
Keyword(s):  
Taxonomic Change

Genomic versus morphologic rates of evolution: influence of morphologic complexity

Paleobiology ◽  
1975 ◽  
Vol 1 (1) ◽  
pp. 63-70 ◽  
Author(s):  
Thomas J. M. Schopf ◽  
David M. Raup ◽  
Stephen Jay Gould ◽  
Daniel S. Simberloff
Keyword(s):  
Cluster Analysis ◽  
Computer Simulation ◽  
Real World ◽  
Evolutionary Rates ◽  
The Real ◽  
Rate Of Evolution ◽  
Taxonomic Change ◽  
Rates Of Evolution ◽  
Evolutionary Changes ◽  
Complex Forms

The degree of perceived taxonomic change in various lineages may be directly related to their general morphologic complexity: more complex forms appear to change more rapidly. “Rates of evolution” as customarily reported by paleontologists may therefore be a poor indication of evolutionary changes in the underlying genome. Two approaches were used to examine this problem. (1) We have estimated the degree of morphologic complexity by using the number of descriptive terms per genus, and per family, for 12 major groups of animals. Three general levels of complexity occur: (i) gastropods, bivalves and ectoprocts have relatively few terms; (ii) echinoids, foraminiferans, ostracodes, nautiloids, corals, trilobites, and brachiopods have an intermediate number of terms; (iii) mammals and ammonoids appear to have a relatively large number of terms. These 3 levels of complexity also increase in rate of taxonomic turnover; i.e., an increasing rate of evolution. (2) Using a cluster analysis based on morphologic similarity, we grouped 200 lineages of a computer-generated phylogenetic sequence according to 4 phenetic bases: 3, 5, 10 and 20 morphologic traits. Groups based on a few characters are longer lived and are commonly polyphyletic in comparison with groups based on many characters. In both the real world and the computer simulation, the bias of differential morphologic complexity may account for the observation that “only complicated animals evolve.” Most paleontologic studies of the “rate of evolution” may tell us more about morphologic complexity than about evolutionary rates of genomes.

scholarly journals Taxonomic Checklists as Biodiversity Data: How Series of Checklists can Provide Information on Synonymy, Circumscription Change and Taxonomic Discovery

2018 ◽  
Author(s):  
Gaurav Vaidya
Keyword(s):  
North American ◽  
Geographical Area ◽  
Bird Species ◽  
Software Tool ◽  
Biodiversity Data ◽  
Taxonomic Change ◽  
Biodiversity Database ◽  
Taxonomic Changes ◽  
North American Bird ◽  
Species Being

Taxonomic checklists are a fundamental and widely-used product of taxonomy, providing a list of recognized taxa within a taxonomic group in a particular geographical area. Series of taxonomic checklists provide snapshots of recognized taxa over a period of time. Identifying and classifying the changes between these checklists can provide information on rates of name, synonym and circumscription change and can improve aggregation of datasets reconciled to different checklists.To demonstrate this, I used a series of North American bird checklists to test hypotheses about drivers of splitting rates in North America birds. In particular, I asked if splitting was predominantly undoing previous lumping that happened during the heyday of the modern synthesis. I found that bird species have been split at an accelerating rate since the 1980s. While this was partially the result of previously lumped species being resplit, most splits were unrelated to previous lumps and thus represent new discoveries rather than simply the undoing of previous circumscription changes. I also used a series of North American freshwater algal checklists to measure stability over fifteen years, and found that 26% of species names were not shared or synonymized over this period. Rates of synonymization, lumping or splitting of species remained flat, a marked difference from North American birds. Species that were split or lumped (7% of species considered) had significantly higher abundance than other species in the USGS NAWQA dataset, a biodiversity database that uses these checklists as an index. They were associated with 19% of associated observations, showing that a small number of recircumscribed species could significantly affect interpretation of biodiversity data.To facilitate this research, I developed a software tool that could identify and annotate taxonomic changes among a series of checklists, and could use this information to aggregate biodiversity data, which will hopefully facilitate similar research in the future. My dissertation demonstrates the value of taxonomic checklists series to answer specific questions about the drivers of taxonomic change ranging from philosophical and technical changes to characteristics of species themselves such as their abundance.

Majority rules, when systematists disagree

2005 ◽  
Vol 18 (1) ◽  
pp. 1 ◽  
Author(s):  
Timothy J. Entwisle ◽  
Peter H. Weston
Keyword(s):  
Interest Groups ◽  
Plant Systematics ◽  
Taxonomic Change ◽  
Strong Interest ◽  
Australian Plant ◽  
Rules Of Thumb ◽  
Majority Rules ◽  
The Creation

The creation of Australia’s Virtual Herbarium forced the Australian plant systematics community to find a mechanism for deciding between alternative taxonomies. Following a workshop on the Orchidaceae and the publication of some simple draft guidelines, a set of ‘rules of thumb’ are presented here that we believe represent the view of most practising systematists. Not everyone will agree, and we have provided alternative views where possible. We include the need for monophyletic taxa, minimising taxonomic change, understanding that some taxa have strong ‘interest groups’, making it clear that ‘preferred name’ does not necessarily imply ‘best name’ on all criteria, avoiding epithets used in possible congeners, and the concept of ‘majority rules’ when states and territories have differing views.

scholarly journals Changes in Dimethylsulfoniopropionate Demethylase Gene Assemblages in Response to an Induced Phytoplankton Bloom

2010 ◽  
Vol 77 (2) ◽  
pp. 524-531 ◽  
Author(s):  
Erinn C. Howard ◽  
Shulei Sun ◽  
Christopher R. Reisch ◽  
Daniela A. del Valle ◽  
Helmut Bürgmann ◽  
...  
Keyword(s):  
Surface Waters ◽  
Nucleotide Sequence Identity ◽  
High Throughput Sequencing ◽  
Phytoplankton Bloom ◽  
Marine Bacterioplankton ◽  
Taxonomic Change ◽  
Sequence Identity ◽  
Sequencing Technologies ◽  
Ecological Implications ◽  
Clustering Criterion

ABSTRACTOver half of the bacterioplankton cells in ocean surface waters are capable of carrying out a demethylation of the phytoplankton metabolite dimethylsulfoniopropionate (DMSP) that routes the sulfur moiety away from the climatically active gas dimethylsulfide (DMS). In this study, we tracked changes indmdA, the gene responsible for DMSP demethylation, over the course of an induced phytoplankton bloom in Gulf of Mexico seawater microcosms. Analysis of >91,000 amplicon sequences indicated 578 differentdmdAsequence clusters at a conservative clustering criterion of ≥90% nucleotide sequence identity over the 6-day study. The representation of the major clades ofdmdA, several of which are linked to specific taxa through genomes of cultured marine bacterioplankton, remained fairly constant. However, the representation of clusters within these major clades shifted significantly in response to the bloom, including twoRoseobacter-like clusters and a SAR11-like cluster, and the best correlate with shifts of the dominantdmdAclades was chlorophyllaconcentration. Concurrent 16S rRNA amplification and sequencing indicated the presence ofRoseobacter, SAR11, OM60, and marineRhodospirillalespopulations, all of which are known to harbordmdAgenes, although the largest taxonomic change was an increase inFlavobacteriaceae, a group not yet demonstrated to have DMSP-demethylating capabilities. Sequence heterogeneity indmdAand other functional gene populations is becoming increasingly evident with the advent of high-throughput sequencing technologies, and understanding the ecological implications of this heterogeneity is a major challenge for marine microbial ecology.

scholarly journals Taxonomic change of two species in the genus Haploclastus Simon 1892 (Araneae, Theraphosidae)

ZooKeys ◽  
2010 ◽  
Vol 46 ◽  
pp. 71-75 ◽  
Author(s):  
Manju Siliwal ◽  
Robert Raven
Keyword(s):  
Taxonomic Change
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