taxonomy

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You know those little things that keep bread bags closed?  Well, the internet would like to tell you about them.  If you’re not doing anything too important right now, I think you should visit HORG (that’s the Holotypic Occlupanid Research Group) and explore a beautiful, obsessive, hilarious taxonomy of occlupanids.

(ht Metafilter)

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Two of our biologists have discovered three new stick insect species in the jungle of Vietnam. One of them, Phryganistria heusii yentuensis, is 32 centimetres long and the second largest insect on earth (even 54 cm with forelimbs stretched out). Only one other stick insect is bigger (Phobaeticus chani from Borneo, almost 36 cm). 

During their expeditions Joachim Bresseel and Jérôme Constant collected also dozens of other yet undescribed stick insect species. In years to come, it will certainly more than double the number of known stick insects in Vietnam. The three newly found species are described in the open-access journal European Journal of Taxonomy.

Stick-bugs live at night and are known for effectively replicating the forms of sticks and leaves. Some species perform a rocking motion mimicking the movement of leaves or twigs.

Joachim and Jérôme have been training Vietnamese biologists to build a reference collection of insects and to identify stick insects. Most stick insects are harmless, but at least three species were reported as serious pests in forests of southern China, sometimes defoliating several ha of forest, with numbers of 5000 stick insects per single tree!

On the news, and again. The sticky insects even appeared on Wired.

Check out more stories from the Royal Belgian Institute of Natural Sciences here on Tumblr.

youtube

It’s here! Watch Episode 2 of Shelf Life, the new series that takes you behind the scenes of the American Museum of Natural History.

In this lithograph print, German Biologist Ernst Haeckel depicts twelve species of hummingbirds. The only place where you can find all 328 species in the wild is the Americas. The taxonomic order bestowed upon the hummers by Linnaeus is a culmination of quaint myths that tie the hummer together with geographically estranged birds: the Egyptian plover and the wren. In the past, these two birds were thought to live life on the edge as crocodile teeth-cleaners - the myth of plover-crocodile symbiosis pervades today. When Europeans heard of the mystical hummers of the New World, an account emerged of the hummer joining the wren and the plover in this thrill-seeking employment. Ingellson then tops this lasagna of myths with a fine layer of cheese: hummingbirds were placed in the order Trochilidae, after Trochilus, the ancient Greek word for plover.

(1) print: Ernst Haeckel’s 1899 collection Art Forms of Nature, Wikipedia Commons
(2) Ernest Ingersoll, Birds in Legend, Fables & Folklore (pre-1923)

A Not-So-Brief Lesson in Taxonomic Nomenclature

Listen up, aspiring and practicing scientists of Tumblr. I’m gonna asplain you a thing.

Everyone with a high-school education should be aware of some simple facts:

  • Life forms have been divided into groups of increasing similarity & relatedness:
  • (Domain)-Kingdom-Phylum-Class-Order-Family-Genus-Species
  • This can be remembered with a simple mnemonic:
  • Delightfully-Kinky-People-Come-Over-For-Group-Sex

This view is simplified. You would not be expected to see anything more complicated without getting a degree in a biological field.

Let me explain some more of the more complicated intricacies:

  • Actually, there are also Super-, Sub- and Infra- groups of most of these classifications.

You are almost certainly familiar with some of the subgroups. For instance, ‘Crustacea’ is a Subphylum.

  • Sub-, super-, and infra- groups can be ignored without consequence, but do help us to organise and understand relationships.
  • These group are usually erected to deal with very complicated taxonomy that would be too simple under traditional separation.
  • When the specific levels are unclear (like when the evolutionary history is so complex that we can’t figure out where to draw the lines), the term ‘Tribe’ is often used. This means very little until true groupings can be assigned, but helps us to organise a bit.

There are very strict rules governing how taxonomic names are composed, set out in the International Code of Zoological Nomenclature. Most of these are too complex for me to get into, but at a simple level:

  • Family names always end in -idae (e.g. Iguanidae, Canidae, Felidae etc.)
  • Subfamily names always end in -inae (e.g. Boophinae, Mantellinae, etc.)

NB: The rules of Botanical Nomenclature are different! They follow the International Code of Nomenclature for algae, fungi, and plants.

  • Plant family names always end in -aceae (e.g. Orchidaceae, Iridaceae, etc.)
  • Plant subfamily names always end in -oideae (e.g. Orchidoideae, Vanilloideae, etc.)

There are some rules about how these things are formatted.

  • All levels except species are always capitalised.

Species is never capitalised. Thus, Pan Troglodytes is wrong, while Pan troglodytes is right.

  • Genus and species are always italicised (note: no other levels are ever capitalised).

For instance, Ailurus fulgens is correct, while Ailurus fulgens is not.

  • Subgenus, when it exists, is always placed in brackets between genus and species. Subgenus is never treated as full genus - while you can call a species by Genus species or Genus (Subgenus) species, you can never call a species by Subgenus species.

So Boophis (Sahona) pauliani and Boophis pauliani are both correct, but Sahona pauliani is never correct.

  • After it has been given its full name once, a species may be referred to by an abbreviated form: the first letter of its genus, followed by its species name.

So I may now refer to Boophis pauliani  as B. pauliani. This is not completely necessary, and it is bad practice to insist upon always abbreviating after the first instance. A happy medium must be found, where the full name is brought in occasionally. This usually happens at the start of a sentence.

It should be noted that when working with several species from different genera which either have the same first initial (e.g. Boophis madagascariensis and Brookesia perarmata), or the same species name (e.g. Boophis madagascariensis and Phelsuma madagascariensis), abbreviation may not be the right way to go. Clarity is key.

Species names are usually one of three things:

  • A description of the species’ appearance or habits, usually using Latin, Greek, or other languages, but almost never English. (e.g. Brookesia superciliaris is a dwarf chameleon with well developed superciliary spines (above the eyes); Guibemantis tasifotsy is a frog with white spots on its sides - tasifotsy is a Malagasy word for white spots, tasy meaning spots, and fotsy meaning white).
  • A tribute to the location where the species is found (e.g. Phelsuma madagascariensis).
  • A tribute to a notable researcher/person/organisation. If dedicated to a single person, these names always end in -i (e.g. Phelsuma gouldi was named in honour of Steven Jay Gould, noted evolutionary biologist and popular scientist).

Bad taxonomists, such as the infamous Raymond T. Hoser, tend to name species in tribute to mundane things, like their children, friends, and pets. This practice is strongly frowned upon but not technically against the rules. However, you are never allowed to name a species after yourself.

Description tributes:

  • When quoting a species name, especially in works that actually deal with taxonomy, usually the authors who originally described that species are listed alongside the species.

For instance: Brookesia stumpffi Boettger, 1894

  • The date is not always necessary:

I could also just say Brookesia stumpffi Boettger.

  • This rule applies in the same way to higher levels of classification (so for example: genus Brookesia Gray, 1865).
  • If the species is no longer in the genus in which it was originally described (it has been moved from one to another), the name goes in brackets.

For example: Brookesia perarmata (Angel, 1933) was originally assigned to its own genus because it is so different from all other dwarf chameleons, but was later brought back into the genus Brookesia due to physical and genetic attributes.

Open Nomenclature:

When species are not easily distinguished based on physical or colour-based attributes, taxonomy gets a bit tricky. To get around this, there are several words that have been used for vague implications:

  • the abbreviation ‘sp.’ refers to a species in a genus (e.g. Uroplatus sp.) that is either not yet described, or was not recognisable to the authors.
  • the abbreviation ‘cf.’ refers to an individual or group of individuals that looked like a species, but whose identity is not 100% (e.g. Uroplatus cf. henkeli).
  • the abbreviation ‘aff.’ refers to a species that is probably not yet described, but has certain aspects that suggest it is most closely related to a certain species (e.g. Uroplatus sp. aff. henkeli).

There are no set rules on how to use open nomenclature, so it’s a bit of a mess and is open to interpretations. Some people use ‘cf.’ and ‘aff.’ interchangeably. Suffice to say that, if it has one of these abbreviations in it, the taxonomy needs a bit of work.

Huge success.

Okay that is all for today’s lesson. I hope you learned some stuff. Sorry it was so long. Taxonomic nomenclature is complicated, but its intricacies are quite fun to wrap your head around.

Ruby Seadragon Makes its Debut as a New Species

The stunning ruby sea dragon has made its debut, marking the discovery of the third species of these exotic and delicate fish ever to be known.

As is somewhat common in the incredibly complex and confusing world of taxonomy, this discovery was made purely by chance when scientists at Scripps Institution of Oceanography at UC San Diego were analyzing genetic and anatomical data on samples from what were once the only two species of seadragon in the world.

When they stumbled upon an unusual tissue sample, curiosity got the better of Josefin Stiller and Greg Rouse of Scripps, as well as Nerida Wilson of the Western Australia Museum (WAM).

The trio quickly requested the full specimen that the WAM had on hand, as well as photographs taken just after it was retrieved from the wild in 2007. What they received was a stunningly bright red seadragon - one vastly different from the frilly oranges of Leafy Seadragons and the yellow and purple hues of Common Seadragons.

Further DNA testing and skeletal analysis verified that, indeed, the trio had a new species before them. They named the creature Phyllopteryx dewysea, also referred to as the “Ruby Seadragon.” Results of their analysis are detailed in the journal Royal Society Open Science.

Photo : Scripps Institution of Oceanography 

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Born in 1707, Carl Linnaeus would rise to such a level of greatness that the philosopher Jean-Jaques Rousseau once said “Tell him I know no greater man on earth,” and was heralded by many of his contemporaries and apostles as Princeps botanicorum - the Prince of Botany. This praise was not without merit: he’s the reason we name almost everything in biology the way that we do. Prior to Linnaeus, the science dealing with naming, organizing, and classifying organisms, called taxonomy, was a disorganized and confusingly complex mess. The word taxonomy is derived from an irregularly-conjugated Ancient Greek word taxis which means arrangement, and the Ancient Greek suffix -nomia, derived from the Ancient Greek word nemein, meaning to manage.

Linnaeus had a passion for botany, and while he went to school to study medicine, his long-term goals always included learning about plants. At 25, he won a grant to travel to Lapland and document the local flora and fauna. While there, he began to classify the flowers he found with what we now know as the bionomial classification system - from the Latin bi, meaning two, and nominus meaning name. Prior to this system, species were given long, many-worded descriptive names, and there were several competing outlines for classifying plants and animals into groups, none of which were particularly accurate or helpful to a scientist not intimate with the specific branch of biology the outline was designed for. 

The binomial classification system uses two identifiers for a species - the “generic name” (also known as its genus), and the “specific” name (also known as the species). Linnaeus introduced this system in his book Systema naturae, first published in 1735. Even though the first edition was basic and just twelve pages long, it introduced to the scientific community a system that was simple, understandable, easy to remember, and easy to add new species to. Throughout his life, Linnaeus and his apostles continued work on Systema naturae, and by its 10th Edition in 1758, it classified over 4400 species of animals, and 7700 species of plants.

Portrait of Carl Linneaus by Hendrik Hollander, 1853, in the public domain.

Image from Haeckel’s Tree of Life in the public domain.

Guest post by Arallyn, a humanoid from the third rock from the sun who is fascinated by science and who runs the fantastic blog biomedicalephemera.tumblr.com when she isn’t filling her mind with scientific trivia. Check out and share her cool blog-she has a great eye!  Someday she will be curating major museums and you will say you remember reading her awesome blogs…

Understanding Phylogenies: Terminology
BY EEPUCKETT MARCH 22, 2014

To understand phylogenies let’s start with some basic terminology (Figure 1).
Taxon (plural: taxa): the species/candy bars we will infer relationships between in a phylogeny
Tips: the terminal unit in the phylogeny. There will be one tip for every taxon included in the phylogeny.
Node: point that joins two groups together. Nodes represent the most recent common ancestor of the two groups that were joined.
Branch: the portion of the tree that joins tips and nodes, or nodes with other nodes. In a cladogram, branches are equidistant between nodes; while in a phylogeny representing time, the length of the branch estimates the amount of time that has passed between evolutionary events.
Clade: A group of similar taxa. Figure 1 represents the peanut clade.
Traits: information about the taxa that may be unique to a single taxon or shared by multiple taxa.

Figure 1- Phylogeny terminology using the peanut clade. This clade has three tips represented by the three candy bar taxa. The clade has five branches and two nodes.


Biologists describe how clades are related to each other using the following terms:
Sister taxa: Two taxa (could be one or multiple species/candy bars) that arise from a common node. (Example- Mounds and Almond Joy in Figure 2) [see above]
Monophyletic: A clade formed by all of the species/candy bars sharing a common ancestral node. (Example- M&Ms are monophyletic)
Paraphyletic: A group of taxon descended from a common ancestral node that does not include all of the taxa descended from that node.
Polyphyletic: A group formed by shared traits even when a single common ancestral node is not shared. (Example- In Figure 2 peanuts independently arise three times on the candy bar phylogeny)


(Full article)

Now I just need to do this with my beverages of choice…

Plurals and Possessives in Taxonomic Nomenclature

Okay this is a serious problem, and people need to listen up.

It is very easy:

  • A species has one name.
  • Only one name.
  • That name is not altered in any way.
  • The spelling on that name is not open to interpretation.
  • It cannot be pluralised. No -s, no -es, no -i, no nothing.
  • You do not alter its declension ever for any reason.
  • The gender of the specific epithet depends on the gender of the genus (if the specific epithet is a Latinized word). It must change if the species is moved to another genus of different gender, but not for any other reason.
  • Genera and species CANNOT be made possessive: Anubias’, Scaphiophryne gottlebei's, etc. ARE WRONG.
  • All taxonomic names can be used as a singular or plural form. Usually singular is preferred.

Here is how you conjugate Anubias, the aquatic plant genus:

  • Anubias plant
  • 100 Anubias plants
  • 1014Anubias plants
  • You could equally say 1 Anubias and 100 Anubias, but it would be less clear.

Here is how not to conjugate Anubias:

  • An Anubia
  • 100 Anubia
  • A bajillion Anubiases

Apparently some people like to call a single Betta a Betta splendenNO.

Betta splendens is always Betta splendens irrespective of how many B. splendens you might be talking about. Taking out the s at the end violates its binomial name and is WRONG.

This rule is true for all genera and species.

Thanks to fishmostly for bringing this up in an ask. I hope this clears it up.

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On the twelfth Day of Taxonomy

My true love sent to me

A riotous display of sea anemones!

To ring in 2015, how could we resist the undersea fireworks of taxonomist and illustrator Ernst Haeckel’s sea anemones from Kunstformen der Natur? A popularizer of the then-recent theory of evolution, German biologist Ernst Haeckel helped put Charles Darwin on the map. His 1866 illustration in Generelle Morphologie der Organismen is often cited as the first published depiction of a phylogenetic tree of all life—a map of the evolutionary development of species.

A copy of Haeckel’s Kunstformen der Natur resides in the Museum’s Rare Book Collection, along with many classics of scientific classification. Satisfy your taxonomy craving on the Shelf Life website, and see more beautiful oceanic illustrations in the new book from Museum Curator Melanie Stiassny, Opulent Oceans

We hope you enjoyed the Twelve Days of Taxonomy—Happy New Year!

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Linnaeus’s Asian elephant was wrong species

Molecular sleuths crack 300-year-old mystery over the identity of the Asian elephant type specimen.

“Natural history museums don’t usually tell their visitors, but they are riddled with wrongly identified specimens. Such errors even occur with important holdings, including plants and animals that serve as the archetypes, or type specimens, for their species — the ones that biologists described when they officially named them.

Taxonomy, the science of species organization, started with Carl Linnaeus, and his species descriptions serve as the basis for all other plant and animal classifications. Linnaeus has been proved correct more often than not, but questions hover over some of the species he classified, including the Asian elephant. Researchers have now confirmed a long-held suspicion that the pickled fetus he used as its archetype was, in fact, that of an African elephant.

Could the pickled fetus he used as its archetype actually have been a different species? A team in Copenhagen decided to find out, unaware they were about to add the final chapter to a centuries old saga.

Uppsala, Sweden, 1753

Carl Linnaeus could hardly contain his excitement over his latest acquisition. “I am pleased that the little elephant has arrived. If he costs a lot, he was worth it. Certainly, he is as rare as a diamond,” the founding father of modern taxonomy wrote in a letter to a friend on 18 May 1753.

At Linnaeus’s urging, King Adolf Frederick of Sweden had bought a fetal elephant preserved in alcohol for his already immense natural history collection. Few Europeans had ever laid eyes on an elephant, and Linnaeus was eager to include the beast in his life’s work, Systema Naturae.

Published in 1735 and updated regularly thereafter, Systema Naturae was a naively audacious index of all known life, organized according to the binomial classification system that Linnaeus formalized. He grouped organisms hierarchically, each described with genus and species names in Latin. Linnaeus’s system hinged on the concept of types — individuals that serves as the archetypes for a species, in much the same way that a platinum–iridium cylinder outside Paris defines the kilogram. And because Linnaeus was the one who came up with this system, which is still used by scientists today, he got to pick the type specimens." (read more).

(Source: Nature)