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Taxonomy Basics

How organisms are named - Taxonomy

• The scientific process of finding out how organisms are related to each other is called "systematics" or "phylogenetics*.
• The system of naming these organisms (once we've determined how they are related to each other) is called "Scientific classification".
• The names given to organisms and categories of organisms is called "nomenclature".

(*these terms are not 100% synonymous- see here for the differences)

Traditionally, Taxonomy is used to name different species of organisms. Taxonomy also applies to Y-DNA and mtDNA, even though we are categorizing variation within a species.

Scientific Classification in the form we know it today, was first consistently used by Linnaeus in 1753. This system of naming species was devised so that each organism would have its own unique name, and if we referred to (for instance) Homo sapiens , we would know precisely what organism was being referred to. Before Linnaeus implemented his system many organisms (eg. plants) could have more than one common name, and an individual name could refer to more than one species of organism.

To put this into context - Linnaeus lived in a historical period in which herbs were often used medicinally. If a particular herb (lets call it "lambs ear") was thought to be good for a specific medical condition, - it could be quite disastrousif there was a completely different type of plant also referred to as "lambs ear" (especially so if the alternative plant had toxic properties)........


Linnaeus formulated this naming system to reduce confusion
.

Over time, this naming system has developed, and has very specific rules on how species are named. Certain procedures need to be followed for taxonomic changes to be valid. A couple of important features of this are as follows:

When a Taxonomist has studied an organism or group of organisms, and a new species needs to be named (or the naming within a group of organisms needs to be changed) the scientist will have a scientific paper published. If the scientific paper is naming a new species, it will contain an official description of the new species. The official species description is written in Latin - Latin is used because it is a language that doesn't change, so that the same words used in a species description written in 1753 will mean the exact same thing in 2007, and also the same in 2261. Again, this is a feature of the naming system intended to eliminate confusion about precisely which organism it is.
For each new species described, there is usually what is called a "type specimen". For plants, these type specimens are usually kept in a herbarium. For instance, many of Carl Linnaeus'"type specimens" are kept in the Linnaen herbarium at the Swedish Museum of Natural History. Whenever a taxonomist/systematist wishes to revise the taxonomy of a group of species, they will usually at some stage examine the original type specimens (as well as a diversity of new specimens). These type specimens are very important in defining the identity of a specific taxa. Proper documentation of any changes in what organisms are included within a taxonomic grouping are very important for any future research done on the taxonomic grouping. Any confusion could compromise the accuracy of research.

To put this into context - In my masters degree research, I was looking at the potential evolutionary impact of three very different seed feeding insect species, on the flowering phenology of a genus of alpine grasses Chionochloa. Most species within the genus Chionochloa exhibit a flowering phenology in which some years there is extremely abundant flowering and in other years there can be no flowering. In one historical research paper it stated that one of the insect species (a moth called "Megacraspedus calamogonus") fed in the inflorescences of Arundo conspicua. Plants within the genus Arundo do not exhibitthe same flowering Phenology as plants in the genus Chionochloa. In modern times, the New Zealand species that were formally included within Arundo are now in Cortaderia, and the species that are currently in Chionochloa were formally in the genus Danthonia. Arundo and Chionochloa therefore represent entirely separate genera. The host specificity of M. Calamogonus would strongly influence my research conclusions.
The host specificity of the Insects feeding in Chionochloa inflorescences would impact on the evolutionary pressures caused by the feeding of each of the insects. By reading through the historically published articles, it seemed that the species of grass that the moth had been found in, was now known as "Chionochloa conspicua" (Arundo conspicua is listed as a synonym of Chionochloa conspicua). This would mean that the moth was a specialist feeder. Specialist feeders would be hypothesized to accentuate the flowering phenology exhibitedby the genus Chionochloa (on the other hand a generalist feeder would select against the flowering phenology exhibited by the genus Chionochloa.)
The biggest twist is that the taxa originally described as Arundo conspicua is not the taxa now known as Chionochloa conspicua. Most specimens originally classified as Arundo conspicua are now classified as either Cortaderia toetoe or Cortaderia richardii. It was just as a bizarretwist of fate that when the species was originally described, the herbarium specimen now designated as the holotype for Arundo conspicua was accidentally a specimen of Danthonia cunninghamii instead. (which is precisely why Danthonia cunnighamii became Chionochloa conspicua - the holotype taxa kept the "conspicua" species epithet rather than the Cortaderia taxa, (which then became Cortaderia richardi). This was according to the principle of the first species name/designation given to a taxa having precedence.
Confused ? - yes... I most certainly was at the time........... But the most important point is that:
Without the proper Scientifically published details of all the nomenclature changes, it would have been impossible to unravel the fact that the plant that M. calamogonous was found feeding on was indeed Cortaderia rather than Chionochloa (meaning that the moth is a generalist not a specialist), and I would have come to erroneous conclusions in my research as a result. This should highlight the importance of full official scientific documentation of all changes to the name of a taxa.
The full scientific documentation of taxonomic changes is of paramount importance to assist those in the future to understand what taxa was being referred to in their past. In our present we might understand precisely what we are referring to (regardless of whether it is documented properly), but people in our future will not have that understanding unless it is documented properly.

Quite often, a revision of the taxonomy of a species/group of species is done in response to observations that the classification of a species/group of species might not fit with the true phylogenetic variation within the group of species, and/or a potential new undescribed taxa is found. Often these initial observations may be made by scientists outside the field of taxonomy (eg. Ecologists). In these instances the Scientist (eg. Ecologist) may document this variation and/or new taxa in some way that is relevant to their scientific study, but they will not arbitrarily revise the official scientific nomenclature to fit the variation and/or name the new taxa with official nomenclature - they leave this to the experts who know how to study and document the variation properly (ie. the taxonomists).

To put this into context - In my masters degree research, one of the seed feeding insects was an undescribed species of Cecidomyiid (a type of Dipteran). Several Ecologists have studied Chionochloa and its seed feeding insects over the years, - but we didn't attempt to name the undescribed species of Cecidomyiid - we left it to the experts who had the proper expertise to know what characters were required to classify it . That species has finally been described this year, because researchers were finally able to obtain male specimens. The unidentified Cecidomyiid was named Eucalyptodiplosis chionochloae - more than 40 years since it was first discovered by an Ecologist.

Taxonomy of Human Y-DNA lineages
more about the YCC nomenclature system can be seen on this page.

In 2003, the Y-chromosome consortium (YCC) devised the way taxonomy & nomenclature would be applied to Y-chromosomal lineages.
Quite obviously, there are several aspects of the traditional system of taxonomy which would not be applicable for Y-DNA (for instance, species descriptions in Latin). However it would be logical to conclude that the same principle of reducing confusion should also apply, - and nomenclature should be used so that there is as little confusion about the lineage being referred to as possible.

Human population genetics is a fast moving field. We note that discoveries are made so quickly that if we were to constantly update the nomenclature, then great confusion could (and does) arise, - as the same Y-DNA lineage could experience several different name changes within a very short period of time. Similarly, the same taxonomic label (eg. R1b1) could be used for several different Y-Chromosome lineages.

Unfortunately, this tends to create significant confusion, - which is contrary to the purpose of the system of Taxonomy as Linneaus devised it.

To put this into context - The consequences of Y-DNA haplogroup nomenclature confusion does not have the same serious consequences as confusion of the names of plants with culinary or herbal properties. Confusion about Y-chromosome nomenclature can however still have a significant negative impact. At one end of the scale it affects individuals wanting to understand more about their Y-DNA (or mtDNA), and at the opposite end of the scale it can have a negative impact on scientific research.

In actual fact the Y Chromosome consortium devised two complementary systems of nomenclature. More information about the two complementary nomenclature systems ( "by lineage" and "by mutation) can be seen on this page. The system which is used most often by genetic genealogists is the "by lineage system".

We note that many scientists who publish scientific papers on Y-DNA use the "by mutation" nomenclature rather than the "by lineage" nomenclature. This is not surprising since the "by mutation" nomenclature is more scientifically robust to alterations in the structure of the phylogenetic tree (and thus corresponds much more closely to the principles of Linnaen Taxonomy).

Systematics v's Phylogenetics

The difference between systematics and phylogenetics is that phylogenetics is a type of systematics. There are two main types of systematics - Phenetics and Phylogenetics.

Phenetic taxonomy is sometimes also called "Numerical Phenetics". When using Phenetic taxonomy, the "characters" chosen can have multiple "character states", and it is not necessary to determine what character state is ancestral v's derived. Pheneticists analyse the data they obtain using various different methods of clustering. This clustering occurs on the basis of similarity. Similarity often is correlated with phylogenetic relatedness, - but sometimes is not. Sometimes character states can be shared via common descent and sometimes character states can be shared due to convergence. The disadvantage of this system is that there is no objectively defined "root" for the tree.
More about Phenetics (and how it relates to the Y-Chromosome) can be found on this page

Phylogenetic taxonomy (also called "cladistics") depends on carefully chosen "characters" for which "ancestral" and "derived" states can easily be determined. The advantage of this system is that a "root" can be objectively determined using "outgroup" comparisons. Character states are shared due to common descent.
More about cladistics (and how it relates to the Y-Chromosome) can be found on this page

To put this into context - The clustering of Y-DNA haplotypes would be directly equivalent to numerical phenetics. Network diagrams produced by programs such as Fluxus from STR data would appropriately be called "network diagrams" or "phenograms". Tree diagrams produced by programs such as "splits tree" or "Phylip" are also more appropriately called "phenograms".
It is scientifically inaccurate to refer to STR clusters as Phylograms, Phylogenies, or Phylogenetic trees. These are tree diagrams that are derived from Cladistic taxonomy. Cladistic taxonomy can only be applied to SNP data and other similar binomial polymorphisms. The reason for this is that rapidly changing "characters" (such as STR's) cannot be used in Cladistics/Phylogenetic taxonomy. This is because clear "ancestral" and "derived" states cannot be objectively determined within the context of the Y-chromosome phylogenetic tree.

Therefore a tree diagram derived solely from haplotype data cannot be accurately described as a phylogenetic tree.

Creative Commons License
This work is licensed under a
Creative Commons Attribution-No Derivative Works 3.0 License.
This work can be freely cited, if it is attributed to:
The J2 Y-DNA project or
Angela Cone (2007)
Msc Evolutionary Ecology
http://www.j2-ydnaproject.net/taxonomy_basics.html