Category Archive 'Taxonomy'

09 Sep 2017

Taxonomic Vandalism

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Presumably Naja nigricincta, the Western barred spitting cobra.

Smithsonian reports that there is a problem these days with taxonomic vandalism.

Imagine, if you will, getting bit by an African spitting cobra. These reptiles are bad news for several reasons: First, they spit, shooting a potent cocktail of nerve toxins directly into their victims’ eyes. But they also chomp down, using their fangs to deliver a nasty bite that can lead to respiratory failure, paralysis, and occasionally even death.

Before you go rushing to the hospital in search of antivenin, you’re going to want to look up exactly what kind of snake you’re dealing with. But the results are confusing. According to the official record of species names, governed by the International Commission of Zoological Nomenclature (ICZN), the snake belongs to the genus Spracklandus. What you don’t know is that almost no taxonomists use that name. Instead, most researchers use the unofficial name that pops up in Wikipedia and most scientific journal articles: Afronaja.

This might sound like semantics. But for you, it could mean the difference between life and death. “If you walk in [to the hospital] and say the snake that bit you is called Spracklandus, you might not get the right antivenin,” says Scott Thomson, a herpetologist and taxonomist at Brazil’s Museum of Zoology at the University of São Paulo. After all, “the doctor is not a herpetologist … he’s a medical person trying to save your life.”

In fact, Spracklandus is the center of a heated debate within the world of taxonomy—one that could help determine the future of an entire scientific field. And Raymond Hoser, the Australian researcher who gave Spracklandus its official name, is one of the forefront figures in that debate.

By the numbers, Hoser is a taxonomy maven. Between 2000 and 2012 alone, Hoser named three-quarters of all new genera and subgenera of snakes; overall, he’s named over 800 taxa, including dozens of snakes and lizards. But prominent taxonomists and other herpetologists—including several interviewed for this piece—say that those numbers are misleading.

According to them, Hoser isn’t a prolific scientist at all. What he’s really mastered is a very specific kind of scientific “crime”: taxonomic vandalism.

RTWT

29 Mar 2017

Identify That Spider’s Genera by the Eyes

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31 Oct 2015

Eastern US Has a New Species

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Coywolf

The Economist discusses the pedigree of the now-ubiquitous Eastern Coyote.

It is rare for a new animal species to emerge in front of scientists’ eyes. But this seems to be happening in eastern North America.

Like some people who might rather not admit it, wolves faced with a scarcity of potential sexual partners are not beneath lowering their standards. It was desperation of this sort, biologists reckon, that led dwindling wolf populations in southern Ontario to begin, a century or two ago, breeding widely with dogs and coyotes. The clearance of forests for farming, together with the deliberate persecution which wolves often suffer at the hand of man, had made life tough for the species. That same forest clearance, though, both permitted coyotes to spread from their prairie homeland into areas hitherto exclusively lupine, and brought the dogs that accompanied the farmers into the mix.

Interbreeding between animal species usually leads to offspring less vigorous than either parent—if they survive at all. But the combination of wolf, coyote and dog DNA that resulted from this reproductive necessity generated an exception. The consequence has been booming numbers of an extraordinarily fit new animal (see picture) spreading through the eastern part of North America. Some call this creature the eastern coyote. Others, though, have dubbed it the “coywolf”. Whatever name it goes by, Roland Kays of North Carolina State University, in Raleigh, reckons it now numbers in the millions.

The mixing of genes that has created the coywolf has been more rapid, pervasive and transformational than many once thought. Javier Monzón, who worked until recently at Stony Brook University in New York state (he is now at Pepperdine University, in California) studied the genetic make-up of 437 of the animals, in ten north-eastern states plus Ontario. He worked out that, though coyote DNA dominates, a tenth of the average coywolf’s genetic material is dog and a quarter is wolf.

Read the whole thing.

Hat tip to Robert Laird.

29 Sep 2015

Exactly What Australia Needed

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KimberlyDeathAdder
Kimberly Death Adder (Acanthophis cryptamydros)

IFLScience reports that a new species of snake –though to be among the ten deadliest in the world— has been discovered in Western Australia.

A new species of viper-like snake discovered in the Kimberley region of northwestern Australia is highly venomous and expertly camouflaged. … [T]he Kimberley death adder is a sit-and-wait predator – ambushing frogs, lizards, and small mammals passing by.

A team led by Simon Maddock from London’s Natural History Museum discovered the new species after analyzing mitochondrial and nuclear DNA of Australian death adders in the genus Acanthophis. Previously, populations from the Kimberley region of Western Australia were thought to be the same species as those occupying the Northern Territory.

The new species name comes from the Greek words “kryptos” for cryptic or hidden and “amydros” for indistinct or dim. The findings were published in Zootaxa [pdf] last month.

The back of this 65-centimeter (26-inch) long snake is a pale orange-brown with 33 dark bands. Like others in its genus, the new snake has a diamond-shaped head and a stout body. But in addition to its unique mitochondrial and nuclear gene sequences, the new death adder can also be distinguished by the slightly higher number of cream-colored scales on its underbelly. These scales are unpigmented except for one to three rows of spots.

Its range within Western Australia extends from the grassy, shrubby woodlands of Wotjulum in the west and Kununurra in the east, and it also occurs on some offshore islands including Koolan, Bigge, Boongaree, Wulalam, and an unnamed island in Talbot Bay. “Surprisingly, the snakes it most closely resembles aren’t its closest genetic relatives,” Maddock said in a statement. The team’s mitochondrial DNA analysis indicates that it’s closely related to the desert death adder, A. pyrrhus, and not the Northern Territory death adders, A. rugosus. Similarities between the Kimberley death adder and others in the area may have come about through evolutionary convergence: They ended up with the same traits because of their similar environments.

It’s unclear how many Kimberley death adders there are in the wild, but according to Maddock, they’re probably quite rare.

16 Apr 2014

English: A Scandinavian Language?

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EnglandMapAD900
Map of England, 900 A.D.

Two linguistics professors recently contended that English ought to be classified as a Scandinavian language. (Norwegian) News in English:

Jan Terje Faarlund, a professor of linguistics at the University of Oslo (UiO), told research magazine Apollon that new studies show English “as we know it today” to be a “direct descendant of the language Scandinavians used” after settling on the British Isles during and after the Viking Age. …

Faarlund and his colleague Joseph Emonds, a guest professor at UiO from Palacky University in the Czech Republic, believe they can now prove that English is a Scandinavian language belonging to the group of northern Germanic languages that also include Danish, Swedish, Icelandic and Faroese, spoken on the Faroe Islands.

Their research and conclusions are brand new and break with those of earlier linguistic professors who believe English is rooted in “Old English,” also known as the Anglo-Saxon language believed brought to the British Isles by settlers from northwestern and central Europe. Faarlund claims Scandinavians settled in the area long before French-speaking Normans conquered the British Isles in 1066.

Faarlund and Edmonds also contend that Old English and modern English are two very different languages. “We think Old English simply died out,” Faarlund told Apollon. “Instead, the Nordic language survived, strongly influenced by Old English.”

While many native English-speakers struggle to learn Norwegian, Faarlund believes it’s no coincidence that Scandinavians, especially Norwegians, learn English relatively easily. “It’s true that many of the English words resemble our own (in Norwegian, for example),” Faarlund said. “But there’s more behind it: Even the fundamental structure of the language is amazingly similar to Norwegian. We often avoid mistakes that others (speaking other languages) make in English, because the grammar is much the same.”

Scandinavian settlers, Faarlund notes, gained control towards the end of the 9th century of an area known as Danelagen, which forms parts of Scotland and England today. Faarlund stressed that “an extremely important geographic point in our research” is that the East Midlands in England, where he says the modern English language developed, was part of the relatively densely populated southern portion of Danelagen.

Edmonds and Faarlund also contend that sentence structure in what developed into modern English is Scandinavian, not western Germanic as previously believed. Both today’s Scandinavian languages place the object after the verb, for example, unlike German and Dutch which place the verb at the end of a sentence. Possessive forms can also be the same in both the Scandinavian languages and English, which also can end sentences with a preposition and split infinitives. While that’s sometimes frowned upon in other variations of modern English such as American English, Faarlund argues it’s not possible in German, Dutch or Old English.

All this, he claims, boosts the similarities between Norwegian and English, for example, and the differences between other Germanic languages and English. “The only reasonable explanation is that English is a Nordic language, and that this language is a continuation from the Norwegian-Danish language used in England from the Middle Ages,” Faarlund told Apollon. “Why the residents of the British Isles chose the Nordic grammar, though, is a matter of speculation.”

22 Apr 2011

What’s In Your Intestine?

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Wired describes a newly published scientific paper offering a new form of human taxonomic classification. This development offers promise of assistance in treating gastrointestinal diseases and obesity and in more specifically personalizing medical treatment in general.

In much the same way that every person has one of eight common blood types, each of us may contain one of several possible bacterial communities, suggests new research. …

In the latest study [Published Apr. 21 in Nature], [Mani] Arumugam, fellow EMBL bionformaticist Peer Bork and dozens of other researchers sequenced every gene they could find in fecal samples from 22 people from Denmark, France, Italy and Spain. Then they searched the data for patterns, looking to see if certain arrangements of bacteria tended to be found in certain people.

The search returned three distinctive “enterotypes,” or bacterial communities dominated by a distinct genus — Bacteroides, Prevotella or Ruminococcus — each of which is found with a particular community of bacteria (see picture above).

“One analogy that people draw — I don’t know how accurate it is yet — is blood type,” said Arumugam. “It’s not exactly the same. Blood types don’t change, but we don’t know if enterotypes do.”

Further analysis of microbiomes from 13 Japanese and four Americans returned the same three clusters, suggesting the patterns are widespread and unconnected to ethnicity, age or gender. With such a limited sample size, however, containing no microbiomes from South Asia, Africa, South America and Australia, it remains to be seen whether other enterotypes exist.

Beyond identifying the enterotypes, “anything we say now will be a hypothesis,” said Arumugam. In terms of function, each of the enterotype-defining genera has been linked to nutrient-processing preferences — Bacteroides to carbohydrates, Prevotella to proteins called mucins, or Ruminococcus to mucins and sugars — but far more may be going on.

“Exactly what they are doing in there is still to be explored,” said Arumugam.

20 Apr 2010

Geek, Dork, Dweeb, Nerd

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GreatWhiteSnark elucidates the conceptual distinction with a Venn’s Diagram.

Hat tip to Ben Slotznick.

15 Mar 2007

Borneo Clouded Leopard a Separate Species

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AP is reporting that DNA testing has established that the Borneo Clouded Leopard Neofelis nebulosa diardi should really be classified as a separate species from Neofelis nebulosa. It will probably be renamed simply Neofelis diardi.

A type of leopard found on the Southeast Asian island of Borneo and believed to be related to its mainland cousin is in fact a completely new cat species, WWF said Thursday.

The conservation group said American scientists compared the DNA of the clouded leopard with that of its mainland cousin and determined the two populations diverged some 1.4 million years ago.

“Genetic research results clearly indicate that the clouded leopard of Borneo should be considered a separate species,” WWF quoted Dr. Stephen O’Brien of the U.S. National Cancer Institute, which carried out the tests, as saying.

The clouded leopard is Borneo’s largest predator, has the longest canine teeth relative to its size of any cat, and can grow as large as a small panther.

There are estimated to be between 5,000 and 11,000 of these animals left in Borneo’s rain forests.

Wikipedia


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