Category Archive 'Taxonomy'
20 Jul 2018
The official history of Earth has a new chapter – and we are in it.
Geologists have classified the last 4,200 years as being a distinct age in the story of our planet.
They are calling it the Meghalayan Age, the onset of which was marked by a mega-drought that crushed a number of civilisations worldwide.
The International Chronostratigraphic Chart, the famous diagram depicting the timeline for Earth’s history (seen on many classroom walls) will be updated.
02 Jul 2018
Fidel Castro was an admirer of the native Cuban predatory reptile, but his conservation efforts, like most of hos grandiose schemes, were mired in contradictions.
Conserving the Cuban croc was one of Fidel Castroâ€™s first priorities after he steamed into power in 1959. Just months into his rule, he ordered the creation of the Criadero de cocodrilos, CiÃ©naga de Zapataâ€”or Zapata Swamp Captive Breeding Facilityâ€”a cluster of ponds, rows of concrete-block pens, and a couple of narrow one-story buildings split into modest offices and workspaces for staff two and a half hours south of Havana. Castro always had a predilection for wild spaces and things, says environmental historian Reinaldo Funes-Monzote of the University of Havana. Whether he cherished endemic species because they fit with his hypernationalistic sensibilities, or he related to their untamed energy, or he was just enlightened to the inherent value of wildlife is a guess, though crocodiles must have become a point of pride for him at some stageâ€”he eventually developed a habit of gifting them, either living or embalmed, to foreign allies. He also launched initiatives to raise manatees, deer, and Cuban gar in the swamp.
The island of Cuba, some say, is shaped like a crocodile, though you need a highly developed imagination to see it. The hatchery, located on one of its webbed feetâ€”whether front or back depends on which way you tilt your headâ€”has been solely dedicated to the conservation of the Cuban crocodile since 1974. The mission is straightforward in theory: secure the Cuban crocodile for the future and learn about the natural history of the little-understood species along the way. Yet as geneticist Yoamel MiliÃ¡n-GarcÃa of the University of Havana and others peer into the crocodileâ€™s cellular secrets, theyâ€™re revealing that thereâ€™s a lot more that needs to be considered when it comes to conserving Castroâ€™s croc.
In the wild, the Cubanâ€”one of the worldâ€™s rarest crocodilesâ€”is found almost exclusively within the 300-square-kilometer freshwater interior of the Zapata Swamp. The saltier stretches along the coast are the domain of Cubaâ€™s other native crocodileâ€”the widely distributed American (Crocodylus acutus), also found in coastal areas across Cuba and other Caribbean islands, and on the mainland from Mexico and southern Florida down to northern Peru and Venezuela. The Cuban is bolder and hunts during the day. It has a stubby snout, a reputation for jumping, and a tendency to walk with its belly high off the ground. The American is bigger, more apt to hide, searches for prey at night, sports dark bands on its back and sides, and has a long, pointed snout and extra webbing on its hind toes. The differences are as distinct as red from blue. Yet when MiliÃ¡n-GarcÃa analyzed their genetics a few years ago, he confirmed what zookeepers and scientists had already suspected: the two species are skinny-dipping in the same gene pool. …
By the time Castro had taken power, Zapata Swamp had already been altered by human ambition. Land reclamation projects here date back to the 19th century. And as researcher Claudia MartÃnez Herrera from Cubaâ€™s national archive explains in a report, in the 1940s, the sugar industry arrived in the swampâ€”trees were cleared to make way for crops and mills and to power production. Loggers also cut swaths of royal ebony, mahogany, and white oak for export and for coal production. The sediment released from logging changed the areaâ€™s hydrology, causing four distinct areas to merge together into one giant swamp. Inhabitants drove artificial channels deep into the interior to access remaining trees. When Fulgencio Batista was in power, he had even taken steps to slash a canal all the way from the swampâ€™s south coast to Havana, bisecting the country, as a shortcut for ships traveling between the United States and the Panama Canal, though it never materialized.
Castro embraced the notion of bringing economic development to the sparsely inhabited and impoverished region. In The Real Fidel Castro, the late former British ambassador to Cuba Leycester Coltman says that from the beginning, the leaderâ€”who has been heralded as an environmentalistâ€”â€œshowed a fatal attraction to gigantic schemes to conquer nature and change the landscape, the sort of projects that appealed to other modern pharaohs such as Mussolini and Stalin.â€ Castro wanted to drain the swamp, a â€œvirtually unpopulated region, infested with mosquitoes and crocodiles,â€ and convert it into â€œa rich area for rice-growing and tourism,â€ Coltman writes. Under his watch, Funes-Monzote confirms, more water was siphoned away and more artificial channels were driven deep into the swamp, into Cuban crocodile habitat.
Aspiring to save endemic species while simultaneously degrading their habitat is clearly contradictory, though awareness about the importance of saving ecosystems rather than focusing on specific species had not yet become part of the zeitgeist, and land reclamation was still generally viewed as a good idea, says Funes-Monzote. Plus, Castro was perfectly comfortable with contradictions. …
[A]lthough they look and behave differently, Cuban crocodiles and American crocodiles in Cuba are almost genetically the same to begin with. Only a 0.9 percent genetic difference exists between themâ€”which makes American crocodiles here much more closely related to Cuban crocodiles than to members of their own species elsewhere in their range. Perhaps considering them two species was a taxonomic miscalculation and they should be treated as one. Or, maybe the American crocodile in Cuba needs to be designated a second crocodile species entirely unique to Cuba. In that case, could allowing two separate but wholly Cuban species to hybridize prove more palatable from a social perspective?
The Cuban croc is probably really only a sometimes-isolated local subspecies, at best.
09 Sep 2017
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 victimsâ€™ 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, youâ€™re going to want to look up exactly what kind of snake youâ€™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 donâ€™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. â€œIf you walk in [to the hospital] and say the snake that bit you is called Spracklandus, you might not get the right antivenin,â€ says Scott Thomson, a herpetologist and taxonomist at Brazilâ€™s Museum of Zoology at the University of SÃ£o Paulo. After all, â€œthe doctor is not a herpetologist â€¦ heâ€™s a medical person trying to save your life.â€
In fact, Spracklandus is the center of a heated debate within the world of taxonomyâ€”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, heâ€™s named over 800 taxa, including dozens of snakes and lizards. But prominent taxonomists and other herpetologistsâ€”including several interviewed for this pieceâ€”say that those numbers are misleading.
According to them, Hoser isnâ€™t a prolific scientist at all. What heâ€™s really mastered is a very specific kind of scientific “crime”: taxonomic vandalism.
31 Oct 2015
The Economist discusses the pedigree of the now-ubiquitous Eastern Coyote.
It is rare for a new animal species to emerge in front of scientistsâ€™ 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 parentâ€”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 â€œcoywolfâ€. 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 MonzÃ³n, 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 coywolfâ€™s genetic material is dog and a quarter is wolf.
Read the whole thing.
Hat tip to Robert Laird.
29 Sep 2015
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 â€“ ambushing frogs, lizards, and small mammals passing by.
A team led by Simon Maddock from Londonâ€™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 â€œkryptosâ€ for cryptic or hidden and â€œamydrosâ€ 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. â€œSurprisingly, the snakes it most closely resembles arenâ€™t its closest genetic relatives,â€ Maddock said in a statement. The teamâ€™s mitochondrial DNA analysis indicates that itâ€™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.
Itâ€™s unclear how many Kimberley death adders there are in the wild, but according to Maddock, theyâ€™re probably quite rare.
16 Apr 2014
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 â€œas we know it todayâ€ to be a â€œdirect descendant of the language Scandinavians usedâ€ 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 â€œOld English,â€ 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. â€œWe think Old English simply died out,â€ Faarlund told Apollon. â€œInstead, the Nordic language survived, strongly influenced by Old English.â€
While many native English-speakers struggle to learn Norwegian, Faarlund believes itâ€™s no coincidence that Scandinavians, especially Norwegians, learn English relatively easily. â€œItâ€™s true that many of the English words resemble our own (in Norwegian, for example),â€ Faarlund said. â€œBut thereâ€™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.â€
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 â€œan extremely important geographic point in our researchâ€ 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 todayâ€™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 thatâ€™s sometimes frowned upon in other variations of modern English such as American English, Faarlund argues itâ€™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. â€œThe 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,â€ Faarlund told Apollon. â€œWhy the residents of the British Isles chose the Nordic grammar, though, is a matter of speculation.â€
22 Apr 2011
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 â€œenterotypes,â€ or bacterial communities dominated by a distinct genus â€” Bacteroides, Prevotella or Ruminococcus â€” each of which is found with a particular community of bacteria (see picture above).
â€œOne analogy that people draw â€” I donâ€™t know how accurate it is yet â€” is blood type,â€ said Arumugam. â€œItâ€™s not exactly the same. Blood types donâ€™t change, but we donâ€™t know if enterotypes do.â€
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, â€œanything we say now will be a hypothesis,â€ said Arumugam. In terms of function, each of the enterotype-defining genera has been linked to nutrient-processing preferences â€” Bacteroides to carbohydrates, Prevotella to proteins called mucins, or Ruminococcus to mucins and sugars â€” but far more may be going on.
â€œExactly what they are doing in there is still to be explored,â€ said Arumugam.
20 Apr 2010
GreatWhiteSnark elucidates the conceptual distinction with a Venn’s Diagram.
Hat tip to Ben Slotznick.
15 Mar 2007
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.