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…

 The origin and diversification of Bushbabies.

 Satellite tracking Pygmy Blue Whales.

 The origin and diversification of modern Lions.

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A new species of Fly from the Mid-to-Late Jurassic of Inner Mongolia.

The True Flies, Diptera, are one of the most successful groups of insects, with around 240 000 described species and a fossil record that dates back to the Triassic. They can be distinguished from other Insects with 'fly' in their names by only having a single pair of wings, the forewings, the hindwings having been reduced to a pair of halteres, which act as gyroscopes during flight. Only the adult Fly has wings; Flies undergo a complete metamorphosis on reaching maturity, the larvae being a worm-like caterpillar. 

In a paper published in the journal ZooKeys on 6 November 2012, Junfeng Zhang of the College of Palaeontology at Shenyang Normal University and the Nanjing Institute of Geology and Palaeontology at the Chinese Academy of Sciences describes a new species of Fly from the Daohugou Formation of Ningcheng County in Inner Mongolia.

The new Fly is considered to be sufficiently distinct to be placed in a new Family, the Orientisargidae (Eastern Flies) and given the specific name Orientisargus illecebrosus, meaning the Enchanting Eastern-Fly. Orientisargus illecebrosus is an elongate, slender Fly, slightly over 12 mm in length, preserved as part and counter-part on limestone slabs.

Orientisargus illecebrosus, part and counterpart, holotype, female, dorsal view. Scale bars 1 mm. Zhang (2012).

Orientisargus illecebrosus, line drawing. Scale bar is 1 mm.

See also Two new species of Corpse Fly from Vietnam, Two new species of Mosquito from the Eocene of Montana, Miocene Quasimodo Flies in Dominican Amber, Males of two species of Horse-fly described for the first time and Two new species of Fungus Gnat from Southeast Asia and Australasia.

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Two new species of Corpse Fly from Vietnam.

Corpse Flies (Phoridae) are small Flies resembling Fruit Flies but with humped backs. They get their name from the fact that some species lay their eggs on human corpses, and their ability to go through several generations within sealed coffins, an ability that makes them invaluable to forensic entomologists (scientists who use the insects colonizing corpses and other evidence to establish a time scale). Other species incubate on a range of decaying organic material, including animals, plants and fungi. A few are parasitoids, with the young growing inside the bodies of Ants or Bees. They are sometimes known as scuttle flies, due to their tendency to run, rather than fly, away from perceived threats.

In a paper published in The Raffles Bulletin of Zoology on 29 February 2012, Gábor Lengyel and László Papp of the Department of Zoology at the Hungarian Natural History Museum describe two new species of Corpse Fly from Vietnam.

The first new species is placed in the genus Abaristophora and given the specific name hirticornis, referring to the hairy antennae the species possesses. The species is described from a single male specimen found in a gorge at the edge of a forest in Hoa Binh Province. It is a 1.3 mm Fly with a brown head and body and yellowish legs.

Abaristophora hirticornis. Male specimen. Scale bar is 0.5 mm. Lengyel & Papp (2012).

The second new species described is placed in the genus Postoptica and given the specific name continetalis, meaning 'from a continent' (Asia); the only previously described species in the genus coming from the island of Sulawesi. The species is described from two male specimens, one from the same location as Abaristophora hirticornis, the other from the Ba Bể National Park in Bắc Kạn Province. Postoptica continetalis is a 4.8 mm dark brown Fly with reduced wing venation and eyes that almost meet.

Postoptica continetalis. Male specimen. Scale bar is 1.0 mm. Lengyel & Papp (2012).

See also Two new species of Mosquito from the Eocene of Montana, Miocene Quasimodo Flies in Dominican Amber, Males of two species of Horse-fly described for the first time, Two new species of Fungus Gnat from Southeast Asia and Australasia and New species of Silver Fly from Brazil.

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Miocene Quasimodo Flies in Dominican Amber.

Quasimodo Flies (Curtonotidae) are small Flies with dull colouration and distinctively humped backs. They are distributed throughout the world, though in most places they are quite uncommon. However in Africa and tropical America they are an abundant and diverse part of the insect fauna. The group have not been extensively studied, and therefore are not well understood.

In a paper published in the American Museum Novitates on 18 October 2012, David Grimaldi Division of Invertebrate Zoology at the American Museum of Natural History and Ashley Kirk-Spriggs of the National Museum in Bloomfontein and the School of Life Sciences at the University of KwaZulu-Natal describe two new species of Quasimodofly from Miocene amber from the Dominican Republic, thought to be 15-20 million years old. Only one fossil Quasimodofly has previously been described (Curtonotum gigas from French Oligocene shale in 1937), and this is now thought to have been erroneously placed, making these new specimens both the oldest and the only known fossils of the group.

The first new species is placed in the pre-existing genus Curtonotum (an extant genus of Quasimodo Flies to which Curtonotum gigas was assigned; the species was removed from the genus and family in 2007 in a paper by Ashley Kirk-Spriggs, but has never been reassigned to another taxon), and given the specific name electrodominicum, meaning from Dominican amber (ēlectron, Greek for amber, plus dominicum, from Dominica). Curtonotum electrodominicum is 7 mm Fly, not significantly humpbacked, named from a single specimen in amber. 

Curtonotum electrodominicum, specimen in amber. Grimaldi & Kirk-Spriggs (2012).

The second new species is placed in a new genus, Depressonotum, meaning flattened, and given the specific name priscum, meaning ancient. The species is named from two specimens, one male and one female, with an average length of 2.77 mm, large eyes and a flattened abdomen. The male is notably more slender than the female.

Depressonotum priscum; (top) female, (bottom) male. Grimaldi & Kirk-Spriggs (2012).

See also A fossil Cricket in Miocene amber, Two new species of Fungus Gnat from Southeast Asia and Australasia, Males of two species of Horse-fly described for the first time and New species of Silver Fly from Brazil. 

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Males of two species of Horse-fly described for the first time.

Horse-flies (Tabanidae) are widespread True Flies (Diptera) noted for their vicious bite, with many species considered to be pests of humans and livestock. Female Horse-flies typically require a meal of mammalian blood prior to reproducing, but males, if they feed as adults at all (like all flies they metamorphose from a totally unflylike form on maturity), feed on nectar or pollen. Because of this many species of Horse-fly are described from female specimens only, with the males being unknown, since only the females are attracted towards humans and domestic animals.

In a paper published in the journal Zootaxa on 16 July 2012, Tiago Kütter Krolow of the Coordenação de Ciências Biológicas at the Universidade Federal do Tocantins, Keith Bayless of the Department of Entomology at North Carolina State University and Augusto Loureiro Henriques of the Coordenação de Pesquisas em Entomologia at the Instituto Nacional de Pesquisas da Amazônia describe the males of two species of Horse-fly previously only known from female specimens. Both species are widespread in South and Central America, but not well studied, and hence are not well represented in entomological collections. 

The first species of Fly to have its male described is Eutabanus pictus, a predominantly black Fly considered to be a mimic of some forms of Flesh-fly (carrion eating Flies in the family Sarcophagidae) though the advantage to this is not clear. The males are described based upon specimens gathered in Brazil and Peru. The males are essentially similar to the females, but with with larger eyes and less prominent abdominal stripes.

Eutabanus pictus. Male (left) and female (right). Krolow et al. (2012).

The second species is Myiotabanus muscoideus, a black and white fly, again considered to be a mimic of some forms of Flesh-fly. The males described are from Mexico (further north than the previously known range of the species) and Guatemala. Again the males are very similar to the females, though the males have a less pointed abdomen and larger eyes.

Myiotabanus muscoideus. Male (left) and female (right). Krolow et al. (2012).

See also New species of Silver Fly from Brazil.

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Two new species of Fungus Gnat from Southeast Asia and Australasia.

Fungus Gnats are small (2-5 mm) flies with larvae that feed on fungi and plant roots, for which reason they are often considered a pest, though most species are essentially harmless. The adults are short lived, but play an important role in the pollination of some plants, and the spread of some fungal spores.

In a paper published in The Raffles Bulletin of Zoology on 29 February 2012, Jan Ševčík of the University of Ostrava and Jostein Kjærandsen of the Museum of Zoology at the Department of Biology at Lund University describe two new species of Fungus Gnat from Southeast Asia and Australasia. 

Both new species are placed in the new genus Brachyradia, which implies 'short radial vein'.

The first species is Brachyradia asiatica, 'Brachyradia from Asia', which was found in Thailand, Malaysia and Sulawesi in Indonesia. Brachyradia asiatica is a 2.4-3.0 mm brownish yellow fly; the males being larger than the females.

Brachyradia asiatiaca. Ševčík & Kjærandsen (2012).

The second species is named Brachyradia australis, the Southern Brachyradia. This is named from specimens from Sulawesi and Papua New Guinea. Brachyradia australis is a 2.0-3.0 mm brownish yellow fly; the females tending to be larger than the males.

Brachyradia australis. Ševčík & Kjærandsen (2012).

See also New species of Silver Fly from Brazil.

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New species of Silver Fly from Brazil.

Silver Flies, Chamaemyiidae, are small True Flies (Diptera) with active predatory larvae, which typically target Aphids or Scale Insects. The group are found worldwide, and have a fossil record dating back to the Eocene.

In a paper published in the journal Zootaxa on 12 June 2012, Stephen Gaimari of the California State Collection of Arthropods at the Plant Pest Diagnostics Branch of the California Department of Food & Agriculture describes a new species of Silver Fly from Sāo Paulo State, Brazil.

The new Fly is placed in the new genus Chamaeleucopis, a combination of Chamaemyia and Leucopis, two previously described genera to which it bears similarities, and given the specific name trevas, which means 'darkness' in Portuguese. Chamaeleucopis trevas is a 2.1-2.2 mm, dark coloured Silver Fly, with larvae that feed on Scale Bugs of the genus Ceroplastes. It was only found living on one species of plant, the guava, Psidium guajava.

A specimen of Chamaeleucopis trevas. Scale bar is 0.5 mm. Gaimari (2012).

See also Three new species of Chewing Lice from Bulbuls in northern Vietnam, A new species of Antlion from China, Two new species of Rove Beetle from Zhejiang Province, China, Snakeflies in amber from the Early Cretaceous of northern Spain and A Hatchet Wasp preserved in Tertiary amber from Mexico.

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