taxonomy

5

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)

4

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 (up to 54 cm with forelimbs stretched out). Only one other stick insect is bigger (Phobaeticus chani from Borneo, which is almost 36 cm long). 

During their expeditions Joachim Bresseel and Jérôme Constant also collected  dozens of other as-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 insects live at night and are known for effectively mimicking the forms of sticks and leaves. Some species perform a rocking motion to imitate 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 stripping several hectares of forest of its leaves, with up to 5000 stick insects per tree!

On the news, and again. The stick-like insects even appeared on the Wired website.

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

youtube

In this episode of Shelf Lifewe’re talking turtles, taxonomy, and the tales a Museum collection can tell.

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)

Bahamas ghost shark (Chimaera bahamaensis)

Chimaerae (ghost sharks) may be the “oldest and most enigmatic groups of fishes alive today”. At one time a diverse and abundant group, their closest living relatives are sharks, though in evolutionary terms, they branched off from sharks nearly 400 million years ago and have remained isolated ever since. Today, they are largely confined to deep water. (Source)

The man who keeps finding new species of shark (BBC)

Dave Ebert has a favourite market in Taiwan. He’s been going there since he was a student 30 years ago.

“I started seeing a lot of species and I was going, ‘What the heck is this?’ And in many cases it was a known species but we didn’t know it occurred here. Then I realised there were some species we didn’t even have names for, they weren’t even known about, and here people were catching them and selling them,” he says.

He has found 10 new species in this market alone. In all, over the past three decades, Ebert has named 24 new species, including sharks, rays, sawfish and ghost sharks - these cartilaginous fish are all related. 

At the moment, scientists know of more than 500 species of shark - a fifth of which have been found in the past decade.

“You really are being an explorer,” says Ebert. “Whether you’re going to a market or going out to sea. Little kids tend to go through that dinosaur and shark phase in life and I never grew out of it. My parents gave me a little shark book when I was about five - I still have it - and I was just fascinated. 

"When I was 10 years old I told my folks, 'I’m going to travel the world and study sharks,’ and they told me to 'follow your dream’. I love it. I get to experience things that most people never will.”

-> David Ebert’s profile

For teaching: marine science

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.

I made a 30 day art challenges cause why not

For 1 month, make and draw a character based off of a species of your choice from each given phylum of animal (some phyla have thousands of species to choose from…others will only have one or two)

You can make them anthros, gijinkas, cartoons, monster, sonic ocs, anything you want as long as it’s at least inspired directly by the critter

The days:

Day 1. Porifera
Day 2. Placozoa
Day 3. Ctenophora
Day 4. Cnidaria
Day 5. Orthonectida or Dicyemida
Day 6. Chaetognatha
Day 7. Platyhelminthes
Day 8. Cycliophora
Day 9. Gastrotricha
Day 10. Rotifera (including Acanthocephala)
Day 11. Gnathostomulida or Micrognathozoa
Day 12. Entoprocta
Day 13. Bryozoa
Day 14. Branchiopoda
Day 15. Nemertea
Day 16. Phoronida
Day 17. Annelida (including Sipuncula and Echiura)
Day 18. Mollusca
Day 19. Priapulida
Day 20. Loricifera  
Day 21. Kinorhyncha
Day 22. Nematoda
Day 23. Nematomorpha
Day 24. Arthropoda
Day 25. Onychophora
Day 26. Tardigrada
Day 27. Xenacoelomorpha 
Day 28. Echinodermata
Day 29. Hemichordata
Day 30. Chordata 

2

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…

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 

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:

  • 1 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.