Biota

Exploring Nature

Classification of life

This project grew out of my trying to label my wildlife photos and identify the species in the pictures. I then wanted to group the photos together based on the species classification. I soon found that this was not as straight forward as I had expected.

Over time, there have been a lot of changes in the classification of life and there is a vast amount of information available about it. Although there are works in progress that are aimed at a unified system of classification, there is still plenty of conflicting information. For help with identifying and classifying my various wildlife observations I have used various sources listed in more details at the end.

I have compiled some general information below, based on notes I made as I was trying to understand the classification systems. There are links to each Kingdom with more information. I will try to update the various sections from time to time but I cannot guarantee that it is all correct or that it is all completely up to date.

Taxonomy

Taxonomy is derived from the Greek words ‘taxis’, which means arrangement, and ‘nomos’, which means method. It is the science of classifying groups of biological organisms into taxa (groups) based on their shared characteristics. Where these groups can be joined by others to make a higher group, a taxonomic hierarchy results.

Animals were first classified by Aristotle (384-322 BC) and he based his classes on their habitat and characteristics. It was Carl Linnaeus (1707-1778) who created the modern ranking system. He proposed the categories Kingdom, Class, Order, Genus and Species. This Linnaean Taxonomy was expanded in the early nineteenth century to include phylum/division and family. This hierarchy has stood the test of time. Although many other categories or ranks have been proposed, the basic hierarchy is still: Domain, Kingdom, Phylum (or Division), Class, Order, Family, Genus, and Species. A good mnemonic for remembering this is: Do Keep Pond Clean Or Fish Get Sick.

Linnaeus also introduced the standardised binomial (Genus and species) naming system that is still in use today. The following bodies govern the international naming protocols or codes:

  • The International Code of Nomenclature1 (ICN) for algae, fungi and plants,
  • The International Code of Zoological Nomenclature2 (ICZN) for animals,
  • The International Code of Nomenclature of Prokaryotes3 (ICNP) for bacteria and archeae
  • The International Committee on Taxonomy of Viruses4 (ICTV)

These rules, or codes, make sure that any organism can be globally identified.

The publication of Charles Darwin’s ‘On the origin of species’ in 1859 led to the classifying of species based on their evolutionary relationships and the concept of phyletic systems. As evolutionary taxonomy is based on Linnaean taxonomic ranks, the two terms are largely interchangeable in modern use.

The cladistics method was introduced in the 1960s. This is a system where organisms are grouped in clades based on their most recent common ancestor. In this system ranks are not required (but are allowed) and the taxa are arranged in a hierarchical evolutionary tree. The advance of molecular genetics is continuing to help fine-tune the placing of clades in the tree.

The naming of clades, which is regulated by the International Code of Phylogenetic Nomenclature5 (PhyloCode), is meant to coexists with the rank-based codes described above.  However, there is much debate about the merit of the phylogenetic nomenclature compared with the Linnaean (and evolutionary) taxonomy. The PhyloCode has not been widely adopted.

Development of Domains and Kingdoms

Linnaeus proposed a two-kingdom (regnum) division, Animalia and Plantae, in 1735.  In 1866 Ernst Haeckel used the term protista for small animal-like and plant-like organisms that are separate from these kingdoms.  Edouard Chatton (1925) organised these kingdoms into the two higher systems (empires) of Prokaryotes (without nucleus) or Eukaryotes (with nucleus). In 1969 Robert Whittaker suggested there should be five kingdoms by adding the prokaryotic kingdom Monera and the eukaryotic kingdom Fungi. Carl Woese and George E. Fox (1977) suggested splitting the Monera into two kingdoms, Archaebacteria and Eubacteria, based on rRNA sequence studies. Later, in 1990, Woese6 proposed the Three Domain System, with the domains Bacteria, Archaea and Eukarya. He argued that although Bacteria and Archaea are both prokaryotes and have many similarities there, there are many differences that justify their being classified as separate domains.

1 Woese's Universal tree of life showing the three domains; Bacteria, Archaea and Eukarya (Woese et al., 1990).
Figure 2.1 Woese’s Universal tree of life showing the three domains; Bacteria, Archaea and Eukarya (Woese et al., 1990).

The domain system was not universally accepted. In 1993, Thomas Cavalier-Smith suggested that the domains Eubacteria and Archaebacteria should be regraded to be kingdoms.  He also proposed a new kingdom, Chromista, separate from Plantae and splitting Protista into Protozoa and Archezoa, thus ending up with an eight kingdom system.  He later revised this system to remove Archezoa as a separate kingdom and treating bacteria as a single kingdom7.  In 2015 K. Ruggiero et al8 suggested the seven-kingdom classification of life that is used by the Catalogue of Life (CoL) and many other international organisations. 

List of ranks used in the hierarchy with the number of taxa per rank
List of ranks used in the hierarchy with the number of taxa per rank8

The seven kingdoms are:

  1. Bacteria (Eubacteria) – Prokaryotes
  2. Archaea (Archaebacteria) – Prokaryotes
  3. Protozoa – Eukaryotes
  4. Chromista – Eukaryotes
  5. Plantae – Eukaryotes
  6. Fungi – Eukaryotes
  7. Animalia – Eukaryotes

Cladification

Phylogenetic tree
A view of eukaryote phylogeny reflecting the classification presented herein9.

The Linnaean-ranked method is not the only way to classify life. Ruggiero’s seven kingdoms is also not universally accepted but does have its opponents, especially regarding the classification in the eukaryotic domain9. The cladistic method is an alternative phylogenetic classification system based on clades and using various super-groups and sub-groups.

The tree shown on the right, taken from Adl et. al.10 (2012), shows the super-groups on the outside in capitals, with the various sub-groups on the inside.

Although both methods for organising life on earth are valid, I find the Linnaean-ranked system, as used by CoL, more informative and much easier to follow than the cladistic. Although the concept of a kingdom is imperfect, and biologists are still trying to improve on it, it is still the most widely used system and the one I have chosen to use.

References and links to interesting resources that I have used can be found at the bottom of this page. There is also a glossary to explain some of the terms used.

Albeit incomplete, I have made an attempt at classifying the species in my photo collection using these resources, the help of friends and various other sources of information that I have found online. The online communities of iSpot and iNaturalist have also been helpful. Where there is conflicting information as to which kingdom an organism belongs, I have mostly used the CoL classification.

Prokaryota

Prokaryotes are single-celled, or colonies of similar celled, organisms whose cell does not contain membrane-bound organelles including a nucleus. The name prokaryote comes from Greek with ‘pro’ meaning before and ‘karyon’ meaning kernel or nucleus.

They are typically microscopic with a diameter in the range of 0.5-5.0μm, although there are exceptions. They can form large colonies visible to the naked eye, eg the cyanobacteria (aka blue-green algae).

Although microorganisms are the most abundant and diverse cellular forms of life on Earth, our knowledge about them is skewed by the minute number that have been cultivated in the lab.

Kingdom Bacteria (Eubacteria)

These are true bacteria and they are found everywhere.  Although some are pathogens, many are essential to life and are also important in the recycling of nutrients.

Most bacteria can be grouped into three types based on their response to oxygen: aerobic (require oxygen), anaerobic (do not like oxygen) and facultative anaerobes (prefer oxygen but can live without). They can also be divided according to how they obtain energy: autotrophs (using light energy, photoautotrophic, to fix carbon dioxide or chemical, chemoautotrophic, using nitrogen, sulphur and other elements) and heterotrophs (acquiring energy from breaking down organic compounds in the environment). They can also be grouped based on staining into Gram-Positive (stains red eg Mycobacterium which causes TB and leprosy) and Gram-Negative (stains purple eg Salmonella).

More information…

Kingdom Archaea (Archaebacteria)

The Archaebacteria (meaning ancient/primitive bacteria) was thought to be bacteria but has now been found to be distinct from bacteria based on their ribosomal RNA (rRNA). The structure of their cell walls allows them to live in extreme environments although not all do so. They also generate energy differently. Not so much is known about the Archaea but, as more is discovered, their classification is changing.

They are often classified according to the environments in which they live: halophiles are salt-loving, thermophiles live in extremely high temperatures, and psychrophiles live in extremely cold temperatures. Methanogens produce methane gas.

More information…

Eukaryota

Eukaryotes are organisms with a membrane-bound nucleus and other organelles. They include many large single-cell organisms and all known non-microscopic organisms.

Protists

All eukaryotic organisms, that are not plants, animals or fungi, used to be placed in the Kingdom Protista.  They include protozoa (with some animal characteristics), algae* (which resemble plants) and slime moulds* (similar to fungi). They also include some of the most serious causes of disease like the malaria parasite* (genus Plasmodium) and the potato blight* (Phytophthora infestans).  Recently, the two separate kingdoms of Protozoa and Chromista were proposed7 but many sources are still placing protozoans together with algae and slime moulds in the kingdom Protista. This can be confusing.

*Now Chromista

Kingdom Protozoa

The Kingdom Protozoa occupies a pivotal position between the ancestral prokaryotic Kingdom Bacteria and the four derived eukaryotic kingdoms, Animalia, Plantae, Fungi and Chromista. They are eukaryotic unicellular organisms.

Kingdom Chromista

The boundary between this kingdom and Protozoa is still controversial. Many organisms previously thought to be protozoa are now classified as Chromista, as are some organisms previously included in kingdoms Plantae and Fungi.

Chromista now includes the kelps and other brown algae (phaeophytes), the diatoms (bacillariophytes), the golden-brown algae (chrysophytes), certain moulds (oomycetes) and even heterotrophic flagellates (the Silicoflagellates). It also includes some of the most serious human decease causing agents like the malaria parasites (genus Plasmodium) as well as agricultural pathogens like potato blight (Phytophthora infestans).  This makes chromists very important for ocean ecology, soil biology, climate stability, agriculture, and medicine, as well as for fundamental understanding of eukaryote evolution and biodiversity.

Kingdom Plantae (plants)

These are a group of mainly multicellular, predominantly photosynthetic, organisms.  Historically, any living thing that was not classified as animal was classified as a plant but now fungi and some algae have been judged to be in their own kingdoms. Green algae are now divided between two divisions (phyla), whereas land plants are split into ten divisions. The land plants can be subdivided into vascular and non-vascular plants. Vascular plants can be further subdivided into seeded and seedless plants.

Further classification and information…

Kingdom Fungi

The phylogenetic classification of fungi divides the kingdom into 7 phyla, 10 subphyla, 35 classes, 12 subclasses, and 129 orders. It includes yeasts, rusts, smuts, mildews, moulds and mushrooms. Classification of fungi below the level of the kingdom is controversial and I have yet to find a single, fully accepted system of fungal classification.  My attempt at classification is based partly on information from the Encyclopaedia Britannica and CoL as well as the British Mycological Society (BMS) for English names.

Further classification and information…

Kingdom Animalia (animals)

The animal kingdom is usually separated into vertebrates and invertebrates. The vertebrates contain only one phylum with 5 classes: Aves (birds), Amphibia (frogs & lizards), Reptilia (snakes), Mammalia (mammals) and Fish. I have photographs of some species in all these classes.

While looking at the classification of birds, I made a comparison of the four major world lists.

Invertebrates are now divided into five phyla and four sub-phyla. I have photos of various species the phylum Arthropoda (spiders, insects, crabs etc).

Further classification and information…

Glossary

A taxonomy is a way to organise something into categories. 

A taxon (plural taxa) is a group of organisms classified as a unit; one or more populations of an organism or organisms are seen by taxonomists to form a unit.

Taxonomic hierarchy is an ordered group of taxonomic ranks used to classify organisms from the general to the specific.

Taxonomic rank is the level of a group of organisms within a taxonomic hierarchy.

A phylogeny also organises things into categories, but implicitly requires that that organisation the reflects an evolutionary relationship of those organisms.

Phylogenetics is a classification system based on evolutionary ancestry: the phylogeny (lineage) of grouped organisms. 

A clade (from Ancient Greek: κλάδος, klados,  meaning branch), is also known as a monophyletic group. This is a group of organisms based on a common ancestor and includes all of its lineal descendants. It represents a single “branch” on the “tree of life”.

Cladistics is a classification system that arranges living things with similar traits together on treelike diagrams. This hierarchical classification shows the evolutionary course of organisms based on their shared characteristics, according to DNA similarities and phylogeny, and places them on a branched diagram called a cladogram (like a family tree).

A Monophyletic taxon is a clade of organisms that includes their most recent common ancestor and all its descendants.

A Paraphyletic taxon – a group of organisms that includes the most common ancestor but leaves out some of the descendants tracing back to that common ancestor. 

A Polyphyletic taxon is a group of organisms that have little in common other than some similar traits.

 

References and links

  1. Turland, N. J., Wiersema, J. H., Barrie, F. R., Greuter, W., Hawksworth, D. L., Herendeen, P. S., Knapp, S., Kusber, W.-H., Li, D.-Z., Marhold, K., May, T. W., McNeill, J., Monro, A. M., Prado, J., Price, M. J. & Smith, G. F. (eds.) 2018: International Code of Nomenclature for algae, fungi, and plants (Shenzhen Code) adopted by the Nineteenth International Botanical Congress Shenzhen, China, July 2017. Regnum Vegetabile 159. Glashütten: Koeltz Botanical Books.
    doi: 10.12705/Code.2018
  2. International Code of Zoological Nomenclature
  3. The International Code of Nomenclature of Prokaryotes (ICNP), International Committee on Systematics of Prokaryotes (ICSP)
  4. The International Committee on Taxonomy of Viruses (ICTV)
  5. International Society for Phylogenetic Nomenclature
  6. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Sciences Jun 1990, 87 (12) 4576-4579.
    doi:10.1073/pnas.87.12.4576
  7. Cavalier-Smith, T. (1998),  A revised six‐kingdom system of life. Biological Reviews, 73: 203-266.
    doi:10.1111/j.1469-185X.1998.tb00030.x
  8. Ruggiero, Michael & Gordon, Dennis & Orrell, Thomas & Bailly, Nicolas & Bourgoin, Thierry & Brusca, Richard & Cavalier-Smith, Thomas & Guiry, Michael & Kirk, Paul. (2015). A Higher Level Classification of All Living Organisms. PLoS ONE. 10.
    doi:10.1371/journal.pone.0119248
  9. Adl, S. M., Bass, D. , Lane, C. E., Lukeš, J. , Schoch, C. L., Smirnov, A. , Agatha, S. , Berney, C. , Brown, M. W., Burki, F. , Cárdenas, P. , Čepička, I. , Chistyakova, L. , del, Campo, J. , Dunthorn, M. , Edvardsen, B. , Eglit, Y. , Guillou, L. , Hampl, V. , Heiss, A. A., Hoppenrath, M. , James, T. Y., Karnkowska, A. , Karpov, S. , Kim, E. , Kolisko, M. , Kudryavtsev, A. , Lahr, D. J., Lara, E. , Le Gall, L. , Lynn, D. H., Mann, D. G., Massana, R. , Mitchell, E. A., Morrow, C. , Park, J. S., Pawlowski, J. W., Powell, M. J., Richter, D. J., Rueckert, S. , Shadwick, L. , Shimano, S. , Spiegel, F. W., Torruella, G. , Youssef, N. , Zlatogursky, V. and Zhang, Q. (2019), Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes. J. Eukaryot. Microbiol., 66: 4-119.
    doi:10.1111/jeu.12691
  10. Adl, S. M., Simpson, A. G., Lane, C. E., Lukeš, J. , Bass, D. , Bowser, S. S., Brown, M. W., Burki, F. , Dunthorn, M. , Hampl, V. , Heiss, A. , Hoppenrath, M. , Lara, E. , le Gall, L. , Lynn, D. H., McManus, H. , Mitchell, E. A., Mozley‐Stanridge, S. E., Parfrey, L. W., Pawlowski, J. , Rueckert, S. , Shadwick, L. , Schoch, C. L., Smirnov, A. and Spiegel, F. W. (2012), The Revised Classification of Eukaryotes. J. Eukaryot. Microbiol., 59: 429-514.
    doi:10.1111/j.1550-7408.2012.00644.x

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