Saturday 26 April 2014

Detecting the presence of Mammal species with Carrion Fly derived DNA.

The Earth has suffered a decline in biodiversity over the past century unprecedented in human history. This has led to a concerted effort to monitor populations of animals in many of the world’s threatened ecosystems. However such efforts are require considerable time-investment from individuals trained in species identification, and in some ecosystems, such as tropical forests, are not guaranteed to find all the species present without considerable invasion of the environment by scientific personnel. The advent of modern technology, such as camera traps and DNA analysis, has helped with the detection of some species, particularly Mammals, which follow predictable trails and often leave traces such as hair or faeces which are amenable to collection for laboratory testing.

Recent studies have been able to obtain the DNA of wild Mammals from Leeches and blood-sucking Flies, methods which have the potential for detecting animals unseen by human observers. However Leeches occupy very restricted environments and blood sucking Flies typically target either a single species or a very limited range of species, which somewhat restricts the possible uses of these methods.

In a paper published in the journal Molecular Ecology on 8 January 2013 2013, a team of scientists led by Sébastien Calvignac-Spencer of Emerging Zoonoses at the Robert Koch Institute in Berlin publish the results of a study of Mammal DNA obtained from Blow Flies (Calliphoridae) and Flesh Flies (Sarcophagidae), collectively referred to as Carrion Flies (an ecological term that implies no taxonomic relationship) collected in the Taï National Park in Côte d’Ivoire and the Kirindy Forest in Madagascar. Carrion Flies regularly visit the faeces and corpses of Mammals as well as open wounds on living animals. They are wide ranging and notoriously indiscriminate in their habits, and therefore are likely to carry DNA from a wide range of Mammalian species.

The Bluebottle Fly, Calliphora vomitoria, a Blow Fly found more-or-less globally. Wikimedia Commons.

The Taï National Park is the largest surviving chunk of the Upper Guinean tropical rainforest. It is home to a diverse assemblage of Mammals, including nine nonhuman Primate species, and has been a site of considerable long-term research effort. Flies were collected in two ways in the forest, firstly from Mosquito Nets around a research station where the bodies of deceased Mammals that had been found in the forest were being dissected, and secondly from traps placed at random in the forest. 

The dissection station was known to have material from five Mammal species present; the African Palm Civit (Nandinia binotata), the Sooty Mangabey (Cercocebus atys), the Western Chimpanzee (Pan troglodytes verus), the Western Red Colobus (Piliocolobus badius badius) and an unidentified species of Shrew (Crocidura sp.). Calvignac-Spencer et al. were able to obtain DNA from all of these species, plus DNA from eleven Mammals not present at the site; the Western Red Colobus and Western Chimpanzee from flies collected at the site before they arrived plus the Diana Monkey (Cercopithecus diana), the Lesser Spot-nosed Monkey (Cercopithecus petaurista), the Olive Colobus (Procolobus verus), two unknown species of Duiker (Cephalophus spp.), an unknown species of Swamp Rat (Malacomys sp.) and three unknown species of Mice (Murinae) (these ‘unknown’ species are not necessarily unknown to science; not every African Mammal species is available in DNA databases for comparison).

Traps set in the Taï Forest itself yielded DNA from seventeen Mammalian species, as well as two non-Mammalian Vertebrates. The Mammals were the Jentink’s Duiker (Cephalophus jentinki), the Maxwell’s Duiker (Philantomba maxwellii), the Pygmy Hippopotamus (Hexaprotodon liberiensis), the Water Chevrotain (Hyemoschus aquaticus), the Little Collared Fruit Bat (Myonycteris torquata), the Hammer-headed Bat (Hypsignathus monstrosus), the Sooty Mangabey (Cercocebus atys), the Diana Monkey (Cercopithecus diana), the Campbell’s Monkey (Cercopithecus campbelli), the Greater Spot-nosed Monkey (Cercopithecus nictitans), the Black and White Colobus (Colobus polykomos), the Western Red Colobus (Piliocolobus badius badius), plus an unknown species of Shrew (Crocidura sp.), an unidentified Porcupine (either Atherurus africanus or Hystrix cristata) and two unknown species of Mice (Murinae). In addition unidentified species of Hornbill (Bycanistes sp.) and Screeching Frog (Arthroleptis sp.) were detected.

Calvignac-Spencer et al. consider the detection of DNA from the Jentink’s Duiker (Cephalophus jentinki) to be particularly significant, as the species is both endangered (there are thought to be less than 3500 individuals surviving in the wild) and highly elusive (a small, camouflaged Antelope living in deep forest). They also note that the study, though of a preliminary nature and intended to test the validity of the technique rather than exhaustively seek specific animals or members of specific groups, was able to detect six of the nine Primate species known to be present in the Taï Forest. Primates are also notoriously hard to detect, as not only are many species small, but because they primarily occupy the canopy layer of forests.

A Jentink’s Duiker, Cephalophus jentinki. Brent Huffman/Ultimate Ungulate/ICUN Red List.

The Kirindy Forest of Western Madagascar is a deciduous tropical dryforest, with a distinctive Mammalian fauna including eight Lemur species. This forest has also been the subject of long-term scientific research, particularly concentrating on the Lemurs.

DNA was collected from flies caught within the Kirindy Forest and analysed. This yielded genetic material from four Mammal species, and one Bird; the Tailless Tenrec (Tenrec ecaudatus), the Fat-tailed Dwarf Lemur (Cheirogaleus medius) and Grey Mouse Lemur (Microcebus murinus) plus an unidentified Euplerid Carnivore (either Cryptoprocta ferox or Mungotictis decemlineata), and the Water Rail (Rallus aquaticus). While this is a less impressive list than for the Taï Forest, it does account for 13% of the known Mammalian biodiversity of the Kirindy Forest (4 of 31 species).

The Fat-tailed Dwarf Lemur, Cheirogaleus medius. Wikimedia Commons.

In all three studies Blow Flies accounted for around 90% of the Flies captured, suggesting that they are the more useful group for this sort of study, although there is no known way (or reason) to target the one group of Flies over the other. None of the Fly species captured in the study (not all of which were identified) seemed to favour any particular Mammal species or group of species, suggesting that the method was truly capable of producing a random sampling of the local Mammalian biodiversity, and that if extended over a longer period of time (or employed as a permanent monitoring system at research stations) then it could potentially identify all Mammal species present in an area. 

Calvignac-Spencer et al. further suggest that the method could be used to detect other organisms, such as Mammalian pathogens. They particularly suggest that they method could be used to monitor outbreaks of wildlife disease such as the 2002-2003 Ebola outbreak that killed many Gorillas in Central Africa.

See also…

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