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1.
Promoters of the PhyloCode have mounted an intensive and deceptive publicity campaign. At the centerpiece of this campaign
have been slogans such as that the Linnaean System will “goof you up,” that the PhyloCode is the “greatest thing since sliced
bread,” and that systematists are “afraid” to propose new names because of “downstream consequences.” Aside from such subscientific
spin and sloganeering, proponents of the PhyloCode have offered nothing real to back up claims of greater stability for their
new system. They have also misled many into believing that the PhyloCode is the only truly phylogenetic system. The confusion
that has been fostered involves several discrete arguments, concerning: a new “method” of “designating” names, rank-free taxonomy,
uninomial nomenclature, and issues of priority. Claims that the PhyloCode produces a more stable nomenclature are false, as
shown with the example of “paleoherbs.” A rank-free system of naming requires an annotated reference tree for even the simplest
exchanges of information. This would be confusing at best and would cripple our ability to teach, learn, and use taxonomic
names in the field or in publications. We would be confronted by a mass of polynomial names, tied together only by a tree
graphic, with no agreed name (except a uninomial, conveying no hierarchy) to use for any particular species. The separate
issue of stability in reference to rules of priority and rank can be easily addressed within the current codes, by implementation
of some simple changes, as we will propose in this article. Thus there is no need to “scrap” the current Linnaean codes for
a poorly reasoned, logically inconsistent, and fatally flawed new code that will only bring chaos. 相似文献
2.
Gerry Moore 《The Botanical review》2003,69(1):2-21
Overviews are provided for traditional and phylogenetic nomenclature. In traditional nomenclature, a name is provided with
a type and a rank. In the rankless phylogenetic nomenclature, a taxon name is provided with an explicit phylogenetic definition,
which attaches the name to a clade. Linnaeus’s approach to nomenclature is also reviewed, and it is shown that, although the
current system of nomenclature does use some Linnaean conventions (e.g., certain rank-denoting terms, binary nomenclature),
it is actually quite different from Linnaean nomenclature.
The primary differences between traditional and phylogenetic nomenclature are reviewed. In phylogenetic nomenclature, names
are provided with explicit phylogenetic definitions, whereas in traditional nomenclature names are not explicitly defined.
In phylogenetic nomenclature, a name remains attached to a clade regardless of how future changes in phylogeny alter the clade’s
content; in traditional nomenclature a name is not “married” to any particular clade. In traditional nomenclature, names must
be assigned ranks (an admittedly arbitrary process), whereas in phylogenetic nomenclature there are no formal ranks. Therefore,
in phylogenetic nomenclature, the name itself conveys no hierarchical information, and the name conveys nothing regarding
set exclusivity.
It is concluded that the current system is better able to handle new and unexpected changes in ideas about taxonomic relationships.
This greater flexibility, coupled with the greater information content that the names themselves (i.e., when used outside
the context of a given taxonomy or phytogeny) provide, makes the current system better designed for use by all users of taxon
names. 相似文献
3.
The ultimate goal of taxonomy is to establish a system that mirrors the 'order in nature'. In prokaryote microbiology, almost all taxonomic concepts try to mirror the whole evolutionary order back to the origin of life with the cell as basic unit. The introduction of the 16S rRNA gene as molecular marker allowed for the first time the creation of a hierarchical taxonomic system based on one practical molecular marker. With the development of new and rapid sequencing technologies a wealth of new data can and will be used for critical evaluation of the taxonomic system. Comprehensive analyses of other molecular markers as well as total or partial genome comparisons confirmed the 16S rRNA based hierarchical system as 'backbone of prokaryote taxonomy' at least at the genus level and above. A tendency is visible to classify novel taxa more and more based on the genotype, i.e. comparative analyses of 16S rRNA and/or other gene sequence data (in multilocus sequence analysis, MLSA) at the genus and the species level, sometimes contrary to the indications of other (often phenotypic) data. The understanding of all the information behind these data is lagging far behind their accumulation. Genes and genomes do not function on its own and can only display their potential within the cell as the basic unit of evolution (and hence taxonomy). It is the phenotype and the natural selection that 'drive' evolution in a given environment. In this context, the 'polyphasic taxonomic approach' should be revisited again, taking into account the novel insights into genomes and other 'omic' sciences in a more strict and detailed context with the phenotype. This approach allows a more holistic view and provides a sound basis for describing the diversity of prokaryotes and has the potential to become the foundation of a more stable, in-depth taxonomy of the prokaryotes. 相似文献
4.
The Macrotermitinae are a large and successful subfamily of fungus-growing termites, characterised by their symbiotic association
with white-rot fungi of the genus Termitomyces. The taxonomy of the subfamily, and in particular of the largest genus Odontotermes, is problematic. We used sequences of the mitochondrial 16S gene from termites occurring in East Africa and Malawi to explore
the phyletic relationships within the genus Odontotermes and to place the genus in the broader context of other fungus-growing termites. We also interpret this phylogeny in relation
to classical morphological taxonomy in the form of absolute and relative dry weights of the sterile castes, and in relation
to innate behaviour as shown by nest architecture and fungus comb structure. This work lays the foundations of a complete
taxonomic revision of the Macrotermitinae.
The phylogeny supports one clear subdivision, here called the “tanganicus” group, within the genus Odontotermes. It also supports the significance of field observations on the structure of fungus combs, as the whole “tanganicus” group
builds fungus combs of the sponge type (or modified forms thereof) which are hardly known elsewhere. Other phyletic relationships
are less clear, the residual sequences being referred to as the “latericius” group. We recognise three probable miniature
species within the “tanganicus” group and another possible one in the residual “latericius group”.
Received 16 January 2007; revised 30 October 2007 and 11 March 2008; accepted 4 April 2008. 相似文献
5.
6.
Species’ life histories are often classified on a continuum from “fast” to “slow”, yet there is no consistently used definition
of this continuum. For example, some researchers include body mass as one of the traits defining the continuum, others factor
it out by analysing body-mass residuals, a third group performs both of these analyses and uses the terms “fast” and “slow”
in both ways, while still others do not mention body mass at all. Our analysis of European and North American freshwater fish,
mammals, and birds (N = 2,288 species) shows the fundamental differences between life-history patterns of raw data and of body-mass residuals.
Specifically, in fish and mammals, the number of traits defining the continuum decreases if body-mass residuals are analysed.
In birds, the continuum is defined by a different set of traits if body mass is factored out. Our study also exposes important
dissimilarities among the three taxonomic groups analysed. For example, while mammals and birds with a “slow” life history
have a low fecundity, the opposite is true for fish. We conclude that our understanding of life histories will improve if
differences between patterns of raw data and of body-mass residuals are acknowledged, as well as differences among taxonomic
groups, instead of using the “fast–slow continuum” too indiscriminately for any covarying traits that appear to suit the idea. 相似文献
7.
8.
Two control units, the switching and the two factor discriminating net are described. They are derived as a consequence of
the enzymic oscillatory behavior induced by substrate “perturbation”.
A complex network encompassing long sequences of metabolic reactions is constructed and the organization of cellular metabolic
activities in well defined “regimes” and “states” inferred. 相似文献
9.
The taxonomic treatment for the grasses of southern Africa was one of the first to be based on computerised data and the DELTA
system. These data, based on over 70,000 herbarium records, are amenable for analysis of species parameters including abundance,
frequency and distribution. This information is suitable for the allocation of species into the seven categories of rarity
proposed by Rabinowitz using a combination of habitat specificity (“Narrow” or “Broad”), population structure (“Sparse” or
“Abundant”) and distribution (“Restricted” or “Widespread”). We compare the species lists obtained for each combination of
these three aspects to published Red Data Lists (RDLs) for southern and South Africa. Ninety-three species are placed in the
most sensitive or potentially threatened category (Narrow habitat, Sparse populations and Restricted distributions; RSN).
This is substantially more than the number of species listed in current RDLs for the region. Chi-square tests indicate a statistically
significant bias in taxa from the Fynbos Biome for three of the categories (RSN, RAN and WSN), from the Savanna Biome for
the WAN category and from the arid Succulent Karoo and Desert Biomes for the RAB category. Analyses of habitat requirements
indicate that many grasses listed (especially those associated with a “Narrow” habitat) are found in some form of wetlands
(ephemeral or permanent), especially those at higher altitudes (montane). Despite concerns about the subjective nature in
determining the boundaries between the categories, this method is shown to provide a meaningful and valuable list of taxa
that require prioritisation for more detailed assessment according to the IUCN criteria. 相似文献
10.
James Maclaurin 《Biology & philosophy》2011,26(1):151-158
In Molecular Models: Philosophical Papers on Molecular Biology, Sahotra Sarkar presents a historical and philosophical analysis of four important themes in philosophy of science that have
been influenced by discoveries in molecular biology. These are: reduction, function, information and directed mutation. I
argue that there is an important difference between the cases of function and information and the more complex case of scientific
reduction. In the former cases it makes sense to taxonomise important variations in scientific and philosophical usage of
the terms “function” and “information”. However, the variety of usage of “reduction” across scientific disciplines (and across
philosophy of science) makes such taxonomy inappropriate. Sarkar presents reduction as a set of facts about the world that
science has discovered, but the facts in question are remarkably disparate; variously semantic, epistemic and ontological.
I argue that the more natural conclusion of Sarkar’s analysis is eliminativism about reduction as a scientific concept. 相似文献
11.
Microbial communities present in diverse environments from deep seas to human body niches play significant roles in the complex ecosystem and human health. Characterizing their structural and functional diversities is indispensable, and many approaches, such as microscopic observation, DNA fingerprinting, and PCR-based marker gene analysis, have been successfully applied to identify microorganisms. Since the revolutionary improvement of DNA sequencing technologies, direct and high-throughput analysis of genomic DNA from a whole environmental community without prior cultivation has become the mainstream approach, overcoming the constraints of the classical approaches. Here, we first briefly review the history of environmental DNA analysis applications with a focus on profiling the taxonomic composition and functional potentials of microbial communities. To this end, we aim to introduce the shotgun metagenomic sequencing (SMS) approach, which is used for the untargeted (“shotgun”) sequencing of all (“meta”) microbial genomes (“genomic”) present in a sample. SMS data analyses are performed in silico using various software programs; however, in silico analysis is typically regarded as a burden on wet-lab experimental microbiologists. Therefore, in this review, we present microbiologists who are unfamiliar with in silico analyses with a basic and practical SMS data analysis protocol. This protocol covers all the bioinformatics processes of the SMS analysis in terms of data preprocessing, taxonomic profiling, functional annotation, and visualization. 相似文献
12.
Jun-Ichi Kojima 《The Botanical review》2003,69(1):44-58
Acceptable methods of defining taxon (or clade) names in the draft PhyloCode, or so-called phylogenetic nomenclature, are
“node based,” “stem based,” and “apomorphy based.” All of them define a clade name by pinpointing a node; whereas node-based
and stem-based definitions require two or more taxon “specifiers” to define names, an apomorphy-based definition requires
two specifiers of different types; namely, a single-taxon specifier and a character specifier. The taxon specifier in an apomorphy-based
definition is completely different from the “type” in the Linnaean system. Taxon (or clade) names in the PhyloCode are characterized
in two entirely different manners: One is a name that does not change, either in its orthography or in the contents of the
taxon referred to by it (or its meaning) over time; the other is a name that is just like a pure mark and thus has no meaning.
Communication through such PhyloCode names is very ineffective or impossible. 相似文献
13.
“Genomic medicine” refers to the diagnosis, optimized management, and treatment of disease—as well as screening, counseling,
and disease gene identification—in the context of information provided by an individual patient’s personal genome. Genomic
medicine, to some extent synonymous with “personalized medicine,” has been made possible by recent advances in genome technologies.
Genomic medicine represents a new approach to health care and disease management that attempts to optimize the care of a patient
based upon information gleaned from his or her personal genome sequence. In this review, we describe recent progress in genomic
medicine as it relates to neurological disease. Many neurological disorders either segregate as Mendelian phenotypes or occur
sporadically in association with a new mutation in a single gene. Heritability also contributes to other neurological conditions
that appear to exhibit more complex genetics. In addition to discussing current knowledge in this field, we offer suggestions
for maximizing the utility of genomic information in clinical practice as the field of genomic medicine unfolds. 相似文献
14.
The web and the structure of taxonomy 总被引:4,自引:0,他引:4
An easily accessible taxonomic knowledge base is critically important for all biodiversity-related sciences. At present, taxonomic information is organized and regulated by a system of rules and conventions that date back to the introduction of binomial nomenclature by Linnaeus. The taxonomy of any particular group of organisms comprises the sum information in the taxonomic literature, supported by designated type specimens in major collections. In this article, the way modern means of disseminating information will change the practice of taxonomy, in particular the Internet, is explored. Basic taxonomic information, such as specimen-level data, location of types, and name catalogues are already available, at least for some groups, on the Web. Specialist taxonomic databases, key-construction programs, and other software useful for systematists are also increasingly available. There has also been a move towards Web-publishing of taxonomic hypotheses, though as yet this is not fully permitted by the Codes of Nomenclature. A further and more radical move would be to transfer taxonomy completely to the Web. A possible model of this is discussed, as well as a pilot project, the "CATE" initiative, which seeks to explore the advantages and disadvantages of such a move. It is argued that taxonomy needs to forge better links with its user-communities to maintain its funding base, and that an important part of this is making the products of its research more accessible through the Internet. 相似文献
15.
Lu Dong Jie Zhang Yue Sun Ying Liu Yanyun Zhang Guangmei Zheng 《Conservation Genetics》2010,11(6):2231-2242
Cabot’s tragopan (Tragopan caboti) is a pheasant endemic to southeast China and is protected under both national and global legislation due to ongoing decline
in population size and increased habitat fragmentation. We investigated the phylogeographic patterns and examined the consistency
between evolutionary units and assumed subspecies taxonomy in this species. Six populations across the whole species presenting
a wide distribution range were sampled and two mitochondrial DNA segments (control region, CR and cytochrome b, cyt b) were used in this study. The results demonstrated a high level of genetic diversity (h = 0.97 in CR and 0.78 in cyt b) and significant differentiation among populations. Phylogenetic analyses strongly indicated two reciprocally monophyletic
clades named the “West group” and “East group” that were not consistent with the present subspecies regional distribution.
The divergence time between the two groups was estimated to be around 5.54 × 105–8.7 × 105 years ago, and the expansion times of the two groups were close (about 3 × 105 years ago), indicating the effect of glaciation in intraspecific differentiation. Based on the results of genetic analyses
combined with geographic isolation and distinct population history, our findings suggest that two management units (MUs) should
be defined in T. caboti for conservation. 相似文献
16.
Claus Orendt Georg Wolfram Zdeněk Adámek Pavel Jurajda Mechthild Schmitt-Jansen 《Biologia》2012,67(1):180-199
Macroinvertebrate communities were investigated along a gradient of heavy industrial and municipal pollution in the highland
Bílina River (Czech Republic). Physico-chemical determinants and ions were monitored and community analysis performed focusing
on taxonomic composition, ecological functioning (feeder and dweller guilds) and water quality metrics, including saprobity
index, BMWP and diversity. Impacted sites differed significantly from reference and from recovered stretches. Chemical data
revealed two main pollution factors, (1) a “salinity determinant”, described best by conductivity and SO42−, and (2) an “organic pollution determinant”, represented best by O2 concentrations and NO2−, all varying locally and temporally. Some metrics and taxa showed significant correlations to abiotic parameters. Functional
communities showed a stronger relationship to the “organic pollution determinant”, suggesting that elevated organic pollution
had a dominating influence on functional community metrics; though other variables may also have an influence in this multistress
environment. On the other hand, there were indications that the taxonomic community was more influenced by ion concentrations
(“salinity determinant”). The gradient from reference sites to polluted sites was weaker in the final sampling campaign. The
results presented here can be used as a reference for assessing future changes in environmental impact from pollution, being
finer and more detailed than assessment according to the EU’s WFD. 相似文献
17.
Linda Van Speybroeck 《Theorie in den Biowissenschaften》2000,119(3-4):187-208
Summary Whereas genetics refers to the study and mapping of linear nucleotide sequences, their mutations and inheritance, epigenetics refers to the structural organization and evolution of the genome. Epigenetic studies indicate that not all heritable information
leading to the phenotype is “inscribed” in the DNA base sequence. In this sense, epigenetics — as the term indicates — goes
beyond genetics, thereby (1) leaving behind the gene-centered view from within molecular biology itself, and (2) urging bio-philosophers
to change their focus from criticizing the central dogma to evaluating new developments in molecular research.
In the epigenetic approach, a hierarchy of genomic contexts can be revealed, consisting basically of an intracellular, an
intercellular, and an organismic level. The first explorations on the organismic level suggest that under certain conditions
the somatic constitution of the organism and how it stands in close interaction with its environment are to be taken into
account as factors influencing the genomic constitution. Depending on the specificity of these conditions, the organism and
its history and actuality can be seen as a crucial genomic context — leading to a more complex perception of the local dynamics and the structure of the genome and its consequences for development
and evolution.
This “organism in the world” view fits well with the philosophical tradition of Developmental Systems Theory, although epigeneticists
seek to enlarge the genetic picture of biology by gradually expanding the range of molecular processes which influence the
genome, thereby decentralizing the sovereign role of the genome, without loosing track of experimental demands. 相似文献
18.
Mitochondrial control region was called “A + T-rich” region in invertebrate. In the study, the general organization of control
region in mitten crab was divided into two major domains: high variable segment and conserved segment. Four conserved blocks
(CSB1, CSB2, CSB3 and CSB4) and two tandem repeat sequences (RT1 and RT2) were defined in control region. There were 116 polymorphic
sites and 84 parsimony information sites in 571 aligned sites of the high variable segment adjacent “tRNA-Gln”, in which 58
stable variable sites were defined between E. j. sinensis and E. j. hepuensis. Conserved domain contained more than two similar repeat units, and length polymorphism of control region was due to the
number difference between the two repeat units (RT1 and RT2). And length polymorphism was a common phenomenon for tandem repeat
in control region in the study. Furthermore, a novel result showed the core nucleotide of RT2 in control region tandem repeat
was C in E. j. hepuensis, but G in E. j. sinensis. It might be a rapid and cost-effective measure of seedlings differentiation in aquaculture. 相似文献
19.
Donald R. Forsdyke 《Theorie in den Biowissenschaften》2009,128(3):157-161
Reconsideration of the term “gene” should take into account (a) the potential clash between hierarchical levels of information
discussed in the 1970s by Gregory Bateson, (b) the contrast between conventional and genome phenotypes discussed in the 1980s
by Richard Grantham, and (c) the emergence in the 1990s of a new science—Evolutionary Bioinformatics—that views genomes as
channels conveying multiple forms of information through the generations. From this perspective, there is conceptual continuity
between the functional “gene” of Mendel and today’s GenBank sequences. If the function attributed to a gene can change specifically
as the result of a DNA mutation, then the mutated part of DNA can be considered as part of the gene. Conversely, even if appearing
to locate within a gene, a mutation that does not change the specific function is not part of the gene, although it may change
some other function to which the DNA sequence contributes. This strict definition is impractical, but serves as a guide to
more workable, context-dependent, definitions. The gene is either (1) The DNA sequence that is transcribed, (2) The latter
plus the immediate 5′ and 3′ sequences that, when mutated, specifically affect the function, (3) The latter two, plus any
remote sequences that, when mutated, specifically affect the function. Attempts, such as that of Scherrer and Jost, to redefine
Mendel’s “gene,” may be too narrowly focused on regulation to the exclusion of other important themes. 相似文献
20.