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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)

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.

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Deep sea ‘mushroom’ may be new branch of life

A mushroom-shaped sea animal discovered off the Australian coast has defied classification in the tree of life.

A team of scientists at the University of Copenhagen says the tiny organism does not fit into any of the known subdivisions of the animal kingdom.

Such a situation has occurred only a handful of times in the last 100 years.

The organisms, which were originally collected in 1986, are described in the academic journal Plos One.

"Finding something like this is extremely rare, it’s maybe only happened about four times in the last 100 years," said co-author Jorgen Olesen from the University of Copenhagen.

He told BBC News: “We think it belongs in the animal kingdom somewhere; the question is where.”

The new organisms are multicellular but mostly non-symmetrical, with a dense layer of gelatinous material between the outer skin cell and inner stomach cell layers. (more)

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…

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.

3
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)

Like works of literature, mathematical ideas help expand our circle of empathy, liberating us from the tyranny of a single, parochial point of view. Numbers, properly considered, make us better people.
— 

Daniel Tammet, on Literature, Math, and Empathy

Check out Brain Pickings to read more on Tammet’s thoughts behind our need to classify, our urge to use numbers and descriptions and lists and taxonomies as a sensemaking mechanism for a life that is otherwise rather confusing.

Cephalopodoptera / Squid Moth

Finland-based artist Vladimir Stankovic has created an awesome series of animated illustrations of an entirely new class of organisms: CephalopodopteraThese beautiful creatures appear to be a combination of various mollusc (Octopuses and squid) and insect (Moths and beetles) species. What a wonderful discovery for the worlds of art and science alike!

"Cephalopodoptera is a newly discovered order of species, a link between molluscs and insects. They live in the deepest underwater caves of the oceans worldwide. With the characteristics and intelligence of moths, beetles, octopuses and squid, these animals have managed to remain hidden for centuries. As we speak, tests and experiments are being carried out in order to know more about these mysterious and elusive creatures…”

Visit Laughing Squid to view many more of Vladimir Stankovic's shimmering and tentacular creatures.

Do you reckon biologists went to Antarctica, saw the large penguins and decided without much hesitation "Those are bigger than the other penguins. We will call them King Penguins," then called it a day, and went back to the ship.
The next day heading out they saw even bigger penguins! Do you reckon they thought: Shit! What will I call these ones? I already named those ones kings… What’s bigger than a king? Emperor maybe? Yeah, that’ll work.
"Guys, we’re naming these ones Emperor Penguins."

A third [evolutionary] advance is in a way the most important, since it is the one used by paleontologists to distinguish reptiles from mammals. The lower jaw of reptiles contains several bones, of which two are important to us. One of these, the dentary, bears the teeth while the other, the articular, smaller and at the hind end of the jaw, forms part of the hinge between the lower and upper jaw (Figure 9-8). The other part of this hinge is the quadrate, a small bone in the head portion of the skull, or cranium. Immediately behind these two small jaw bones is the middle ear, within which sound waves are amplified and transmitted from a special nerve to the brain. In reptiles, amphibians, and fishes, this amplification is carried out by a single small bone. By contrast, the lower jaw of mammals consists only of the tooth-bearing (dentary) bone, which is hinged to another bone, the squamosal, also in the cranium. The two bones that form the hinge of the reptilian jaw have not disappeared. They are represented in mammals by two small bones in the middle ear connected with the counterpart of the single reptilian ear bone. In reptiles, amplification of sound waves in the middle ear, carried out by a single bone, is relatively inefficient. The three bones in the mammalian ear do this job much more effectively, so that the hearing of mammals is much better than that of reptiles.

In order to classify fossil animals neatly and clearly as either reptiles or mammals, most paleontologists and nearly all textbooks classify as reptiles all bony-limbed animals that have a liquid-filled amniotic egg and a jaw hinge formed by the two small bones, articular and quadrate, along with a single ear bone. Mammals differ in having the tooth-bearing (dentary) lower jaw bone articulated directly with a bone of the cranium (squamosal), plus three small bones in the middle ear. Tooth structure also helps in classifying them. Nevertheless, an animal that has almost mammalian teeth but a reptilian jaw hinge and middle ear bone is called a reptile. Mammallike reptiles are all classified as reptiles on the basis of this character, even though the advanced dog-tooth has teeth that resemble those of primitive mammals more than they resemble the teeth of the earliest mammallike reptiles or their immediate ancestors, the pelycosaurs. Likewise, the earliest animals having three bones in the middle ear are called mammals, although, like the primitive mammals of modern Australia—the spiny anteater and platypus (monotremes)—they may well have laid eggs, lacked nipples or teats, had skeletons showing some reptilian features such as shoulder girdles, and had chromosomes resembling those of reptiles.

Stebbins - Darwin to DNA, Molecules to Humanity, pp. 289-91

I find this strangely profound: everyone knows the difference between a reptile and a mammal upon seeing one, but once all the fragile details are stripped away, there’s only a single, trivial difference between them; it’s this one silly little criterion that informs all of our (taxonomical) knowledge about species long-extinct. I suspect that the taxonomies of many disciplines are like this.

The text alongside fig. 9-8 reads:

Figure 9-8.
A series of skulls showing a few of the numerous transitional forms that, via a series of adaptive radiations, resulted eventually in the origin of modern mammals (a)–(c): Three typical reptiles. (a) A primitive Captorhinus that, like early amphibians and modern turtles, has only one pair of openings in the skull in addition to the nostrils. (b) A primitive ancestor of lizards, Youngina. (c) A modern lizard, Varanus. (d)–(i): Six reptiles that were on or near the line leading to mammals. (d) and (e) Two pelycosaurs that were typical reptiles but show the beginnings of tooth differentiation. Note that the hindmost bone of the lower jaw (angular, a) is nearly as large as the tooth-bearing bone (dentary, dn). (f) and (g) Two early mammallike reptiles, showing further tooth differentiation, plus reduction in size of the angular bone. (h) and (i) Two later forms of reptiles that, with respect to tooth differentiation and reduction of the angular bone, were much like mammals. Diarthrognathus was almost completely intermediate between reptiles and mammals. (j)–(l): Three kinds of mammals. (j) Sinoconodon, the earliest of these, still retained a number of reptilian features. (k) A later form, Deltatheridium, was very similar to modern shrews. (l) A modern opossum (Didelphys). The skulls are drawn at different scales of magnification. Those in the center column are at natural size or somewhat reduced; those in the right column are somewhat magnified.

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