Biology News Archive

January 2017

An echolocating dormouse

Bats are well known for their ability to navigate using echolocation, but they are not the only mammals to do so. There have been reports of echolocation in shrews finding their way on the forest floor, but these are mostly questionable. New research provides a clear demonstration of echolocation in a dormouse.

The Vietnamese blind dormouse Typhlomys chapensis produces ultrasonic squeaks which are superficially very similar to the noises made by bats. The new research shows that they are able to navigate their way around in complete darkness using these sounds. They are much quieter than the calls made by bats and cannot be picked up by an ordinary bat detector. As they are used by the dormice to navigate their way around while climbing they do not need to be particularly loud, unlike bats which need to know what is further ahead of them while they fly. Quiet calls presumably also minimise the risk of a predator locating the squeaking animal. It turns out that this echolocation is essential for the dormice as they are effectively blind. Although their eyes are functional the retinas are highly folded, meaning that they can detect light but not form an image.Vietnamese pygmy dormice

The Vietnamese pygmy dormouse is an obscure, and evolutionarily isolated species. There is only one other species in the genus (until recently they were thought to be subspecies). Along with one other monotypic genus, they belong to the family Platacanthomyidae, an early branch of the mouse superfamily Muroidea. Platacanthomyids range from mountain forests from India to Vietnam and South China.

The Vietnamese blind dormouse is described as a 'semi-fossorial semi-arboreal' species, which sounds rather contradictory. The reality seems to be that it is a tree climbing species but can burrow. It may have had a more burrowing ancestor, which might explain the loss of vision that forces it to adopt the echolocation.

Photo of two Vietnamese pygmy dormice in Moscow Zoo by Klaus Rudloff (

Source: Panyutina, A. A., Kuznetsov, A. N., Volodin, I. A., Abramov, A. V. and Soldatova, I. B. (2017), A blind climber: The first evidence of ultrasonic echolocation in arboreal mammals. Integrative Zoology. doi:10.1111/1749-4877.12249

February 2017

Mammals ears evolved four separate times

The ears of mammals are special in that the middle ears contain three bones that transmit sound to the inner ear (malleus, incus and stapes), whereas all other vertebrates have just the one (stapes). Fossils and developmental studies have shown that the malleus and incus are derived from bones of the jaws. However, how this occurred was not known. Furthermore, differences between the ears of monotremes (duck-billed platypus and echidnas) suggests that the changes may have evolved twice.

short-tailed opossumNew research into the grey short-tailed opossum Monodelphis domestica has shown that the gene TGF-ßR2 plays a key role in the development of the mammalian middle ear. The cartilage that ossifies into the reptilian lower jaw (Maeckel's cartilage) does so under the influence of this gene. Normal function sees ossification starting in specific centres and then spreading to solidify the jaw. An increase in expression of the gene causes death of the cartilage cells between the ossification centres. The result of this is the formation of the malleus and incus as separeate bones, isolated from the main part of the jaw.

Reconstructing the evolution of the ears based on fossils showing the ear bones or the Maeckel's cartilage suggests that this process occurred separately on four occasions: in the monotremes, the extinct multituberculates, marsupials and placental mammals. With only a single gene change this repeated evolution would be very easy.

Source: Urban, D.J., N. Anthwal, Z.X. Luo, J.A. Maier, A. Sadier, A.S. Tucker & K.E. Sears. 2017. A new developmental mechanism for the separation of the mammalian middle ear ossicles from the jaw. Proc. Biol. Sci. 284(1848). doi: 10.1098/rspb.2016.2416.

Photo by Dawson (CC 2.5)

March 2017

Inbreeding killed the mammoths

The disappearance of the last mammoth species, Mammuthus primigenius, at the end of the last Ice Age 12,000 years ago is easily attributed to the warming climate. It is easy to imagine these woolly giants overheating as the ice retreated. The occasional discovery of a mammoth entombed in ice in Siberia may be a relic of earlier times when conditions were colder and mammoths more plentiful.mammoth

That simple story is complicated by the fact that the very last mammoths just about survived into historical times. The most recent remains are 3,700 years old, from the islands in the Arctic Ocean. These islands stayed relatively cold and mammoth survival seems plausible there. A new study of the remains of these, and other mammoths has uncovered something of their population history.

Genetic analysis shows that the island mammoths were genetically odd in comparison to the great Siberian populations. They had a number of mutations, including ones associated with the sense of smell, digestion and their woolly coat. Rather than being woolly mammoths the very last survivors would have been better described as 'silky mammoths'. None of these mutations would have been beneficial, and what seems to have happened is the inevitable effect of genetic drift in small isolated populations. Instead of mutations being selected out as would be expected in a large population, in small ones they immediately make up a larger proportion of the population and so are less likely to be lost. These mutations build up in the population, and may mean that the population persists but is progressively weakened.

Source: Rogers RL, Slatkin M (2017) Excess of genomic defects in a woolly mammoth on Wrangel island. PLoS Genet 13(3): e1006601. doi:10.1371/journal.pgen.1006601

May 2017

Posion arrow frogs will do anything to avoid cannibals

Many poison arrow frogs of the Amazon breed in epiphytic bromeliads. frogMales carry the eggs up into the tree canopy and deposit them in the isolated pools of water held by the bromeliads. Males of the species Ranitomeya variabilis return after a few days and remove one tadpole, moving this one to another bromeliad. Over several days they distribute the tadpoles around the canopy so there is only one tadpole per bromeliad. If the tadpoles are left together they become cannibals and this behaviour of the males prevents this from happening.Not surprisingly, the tadpoles are desperate to avoid being left together and it has now been found that they will try and jump onto the backs of any frogs that come near.

Source: Schulte, L. M. and Mayer, M. (2017), Poison frog tadpoles seek parental transportation to escape their cannibalistic siblings. J Zool. doi:10.1111/jzo.12472

Photo: John P. Clare

August 2017

A radical new estimate for the number of species on Earth

No-one knows how many species exist. Up to 2 million have been described but it is probable that this is dwarfed by the undescribed and undiscovered. Estimates of the total number vary widely and although some early estimates were as high as 54 million, recently 8-10 million has started to seem like a vague consensus view. However, there have been recent suggestions that the total may be as high as a trillion. These differences are due to variation in approaches and whether the figures are restricted to the largely multicellular eukaryotes (8-54 million) or include micro-organisms as well (up to a trillion).

A new study comes up with a figure of 2.2 billion for all living organisms. For animal species their starting point is a consensus estimate for arthropod diversity of 6.8 million (we have no idea if this figure is right or not) and then consider how many more unrecognised species are indicated by recent DNA based studies. There appear to be almost 6 times as many 'cryptic' species as morphologically recognisable ones, giving 40.8 million arthropods.They then assumed that each arthropod species also had a specialist mite and nematode parasite or commensal associated with it. This puts animal diversity to 163 million animal species (all other animal groups seem to be much lower diversity and so don't really affect the figures).

For plants they used a consensus estimate of 340,000 species. There is much less information on fungi but as this group includes parasites of animals they assumed that each of the 162 million animal species contained at least one parasitic fungus. To this they added an estimated 2.4 million soil fungi, to give 165.6 million fungi.

Protists are even more problematic, and again the parasitic approach was used, with the assumption that each animal hosts one protist, with another 1 million free-living protists estimated. Bacteria were given a higher diversity with the assumption of nearly 11 specialist bacteria per animal and possibly 10 million free-living bacterial species.species diversity landscape

All of this adds up to 2.2 billion species. They varied the assumptions under four different scenarios coming up with a range of estimates from 1.4 to 5.8 billion. This new study is based on major assumptions (the number of arthropods and plants and the number of parasites/commensals per host) which cannot be tested reliably until we have counted the real number of species. From this it may seem little more than guess-work, but it does make a very important point. That is, in estimating the diversity of life so far we have massively under-estimated the number of parasites and micro-organisms. Taxonomy and the speculation over species numbers is highly biased towards the conspicuous and charismatic: vertebrates, some insects and trees. Evaluating and conserving biodiversity requires us to pay much more attention the less charismatic, but more important mites, nematodes, fungi and microbes.

Source: B.B. Larsen, E.C. Miller, M.K. Rhodes & J.J. Wiens. 2017. Inordinate Fondness Multiplied and Redistributed: the Number of Species on Earth and the New Pie of Life. The Quarterly Review of Biology 2017 92:3, 229-265

September 2017

Which animals sleep? - jellyfish do

All vertebrates sleep but it is not clear whether invertebrates do. Arthropods and nematodes have something like sleep and a new study extends the known sleeping animals to jellyfish. The upside-down jellyfish Cassiopea, along with other cnidarians, have periods of inactivity that could be considered 'sleep'. During the night they become inactive. If roused from this state they are slow to respond, as if 'sleepy'. If prevented from sleeping they become less active and responsive. All of these are features of what we recognise as sleep.

upside-down jellyfish

This suggests that all animals with nervous systems have some form of sleep. This makes sense, in that almost all organisms will be exposed to periods of activity and inactivity caused by their food supply. All physiological processes (including nerve activity) will inevitably develop some degree of circadian rhythm. In nerves this will result in varying degrees of responsiveness - periods of wakefulness and sleep. So sleep occurs even in animals without brains.

Source: R.D. Nath, C.N. Bedbrook, M.J. Abrams, T. Basinger, J.S. Bois, D.A. Prober, P.W. Sternberg, V. Gradinaru, L. Goentoro. 2017. The jellyfish Cassiopea exhibits a sleep-like state. Current Biology

October 2017

A 75% decline in flying insects in Germany

A 27-year study of flying insects in German nature reserves has found a dramatic decline in insect abundance, even in protected areas. decline in flying insects Repeated sampling with Malaise traps in 63 nature reserves gave a total of 96 data points (combinations of years and sites). This makes it the most extensive study of insect population changes.

Taking into seasonal effects into account they found a 6.1% annual decrease in flying-insect biomass, and an overall decline of almost 77%. These results are in agreement with other studies which have found major declines in bees, butterflies and moths in different parts of Europe.

This change cannot be explained by changes in weather or habitat within the study sites. It has been suggested that land-use changes (including drainage and pesticide use) in surrounding areas may have had an impact.

This decline is of major significance due to the great role played by flying insects in ecosystems, most fundamentally in pollination.

Source: C.A. Hallmann , M. Sorg, E. Jongejans, H. Siepel, N. Hofland, H. Schwan, W. Stenmans, A. Muller, H. Sumser, T. Horren, D. Goulson, H. de Kroon. 2017. More than 75 percent decline over 27 years in total flying insect biomass in protected areas. PLOSOne

November 2017

A new species of orangutan the new orangutan

A third species of orangutan has been described from the island of Sumatra. The Tapunali orangutan Pongo tapanuliensis is found in a tiny area south of Lake Toba. With its restricted range and a population of just 800 animals, this species immediately became the most threatened ape species. Bornean orangutan P. pygmaeus and Sumatran orangutan P. abelii were separated as species in 1996. Now the population from Batang Toru, south of Lake Toba, is recognised as distinct on the basis of genetic data, skull and dental features. In general appearance there is little difference between this and the other Sumatran species: it is described as having frizzier hair, a prominent moustache and downy hair on the facial flanges of the males. Genetically this species is closer to the Bornean species than to other individuals on Sumatra. This will have arisen as a result of the isolation of different populations: first the Lake Toba isolating the northern Sumatran abelii around 3.4 million years ago and then the separation of tapanuliensis from the Bornean pygmaeus with habitat change on the Sunda shelf 674,000 years ago.

All recent studies list seven species of living non-human great ape: the three orangutans, chimpanzee Pan troglodytes, bonobo P. pansicus and eastern (Gorilla beringei) and western (G. gorilla) gorillas. Genetic studies indicate that there was gene flow between chimpanzees and bonobos possibly until 200,000 years ago, and between gorilla species until around 25,000 years ago. Given how recently there was gene flow between some of these and how similar they are morphologically considering these as 'species' may seem questionable.

The standard definition of a biological species is that it is a group that is reproductively isolated from similar groups, implying that they are unable to breed with related species, or that they produce sterile hybrids. This is not strictly accurate, as many clearly distinct species are able to produce hybrids and whilst many hybrids have reduced fertility, some may be fully fertile. This seems to be the case with the great ape 'species' as Bornean and Sumatran orangutans hybridised in zoos before their distinctiveness (and hence the need to conserve their genetic identity) was realised. There are also records of hybrids between eastern and western gorillas, and between chimpanzees and bonobos. Of these, the only species pair with notable morphological distinction is that of the chimpanzee and the bonobo. This is also the oldest split. It could be argued that the others are only separated as species because they are apes, and we naturally have a particular interest in the diversity of our close relatives.

Source: A. Nater et al. 2017. Morphometric behavioral, and genomic evidence for a new orangutan species. Current Biology 27(22):3487-3489. PLOSOne

Photo: Tim Laman. Published under the Creative Commons Attribution 4.0 International license.

March 2018

Strange adaptations of cave fish the new orangutan

The Mexican tetra fish Astyanax mexicanus is found in rivers and caves in Mexico and Texas. River populations have entered caves and adapted to living in them on at least five separate occasions. Many of these cave populations have converged in being white, blind fish. It is now known that they have also converged in an odd biochemistry.

Life in cave is isolated from the daylight rhythms of the outside world and tends to have little in the way of food. The cave fish have adapted to a periodic bonanza of food washing into caves by becoming better at coping with dramatic changes in food supply. When starved they lose less weight than surface fish do due to a lower metabolic rate and greater fat storage ability.

The cave fish do have higher blood glucose levels, which suggests that something has changed in their control of blood sugar levels. Normally this is regulated by insulin causing glucose to be absorbed from the blood and by glucagon causing its release from stored glycogen. Studies of the fish found that the pancreas development and glucagon use were normal, but that insulin was having less effect than it did in the river fish. This reduced insulin sensitivity can be traced to a point mutation in the insulin receptor gene, the same mutation that produces the insulin resistant Rabson-Mendenhall syndrome in humans. There seems to be more to the story as this mutation did not explain all the effects, so other genes must be involved. Another contributor is a mutation of the melanocorticoid 4 receptor, increasing the appetite in cave fish. All this adds up to give cave fish large, fatty livers.

Fish from one cave differed; in Molino cave they had exceptionally high blood glucose levels and reduced those levels more slowly when starved. This extreme adaptation was not caused by the same insensitivity to insulin. This is the most recent population to have moved into caves and has presumably converged on similar fat storage abilities using a different aspect of their physiology, as yet unidentified.

In humans insulin resistance and hyperglycaemia are associated with type 2 diabetes and would be expected to result in weight loss, rather than fat storage. The new paper observes the apparent contradiction but does not consider it further. It is likely that there are further adaptations that enable the fish to tolerate the high levels of blood glucose and to convert some of it to glycogen, without requiring insulin.

These mutations may have other effects. Hyperglycaemia in humans increases the risk of retinal damage and it is possible that if high levels of blood glucose in the cavefish have similar effects, this may contribute to the repeated reduction and loss of eyes in different populations. The insulin mutation in zebrafish reduces the size of scales, as is the case in wild cave fish. Scale reduction and loss is a common phenotype in different species of cave-dwelling fish, perhaps as a side effect of convergence for greater fat storage.

Source: Riddle et al. 2018. Insulin resistance in cavefish as an adaptation to a nutrient-limited environment. Nature doi:10.1038/nature26136

Photo: Courtesy of Nicolas Rohner

April 2018

New evidence on the origins of mitochondria the new orangutan

Mitochondria, the organelles often referee to as 'power-houses' of the cell are vital structures for almost all living eukaryotes. It is widely accepted that they originated through an endosysmbiosis event, where an oxygen using bacterium was taken up by a larger, anaerobic archaeal cell. Originally this was viewed as being of mutual benefit; the bacterium gained resources and protection from its host while the archaean was able to survive in increasingly oxygen-rich environments. Since the advent of gene sequencing our views of the identity of the bacterium and archaean have been refined. The mitochondria seem to be related to the Alphaproteobacteria while the host cell is now firmly placed in the bizarre Asgard group of Archaea. For the mitochondria, the closest relationship within the Alphaproteobacteria has been identified as the Rikketsiales. This is interesting because many of these are symbionts or parasites, raising the possibility that the original even was not endosysmbiosis, but parasitism.

The most thorough comparison of mitochondria and Alphaproteobacteria has just been published, concluding that the relationship is not as close as had been thought. In fact, mitochondria seem to lie outside the Alphaproteobacteria, suggesting an origin from some other bacterium related to that group. At present it is impossible to say what this means, other than there is no longer strong evidence of a parasitic origin for mitochondria.

The big problem with all of these studies is how little we know about bacteria; this new study included 40 Alphaproteobacteria genomes, many sampled from environmental DNA from sea-water, rather than from individual bacteria. Whilst this is a great increase in sampling, it remains a miniscule fraction of the group. It is highly likely that future studies will change the story yet again.

Source: Joran Martijn, Julian Vosseberg, Lionel Guy, Pierre Offre & Thijs J. G. Ettema. 2018. Deep mitochondrial origin outside the sampled alphaproteobacteria Nature (2018) doi:10.1038/s41586-018-0059-5


Justin Gerlach by e-mail