Chinchilla Rat Extant not Extinct

In an error-strewn article The Guardian (not my favourite newspaper) carried the report on Friday that Cuscomys oblativa, a chinchilla rat or chinchillone, has been found alive.

Hiram Bingham—of Macchu Picchu fame—found skulls of this species in Inca pottery in 1912. Somebody decided that the species must have become extinct but as is so often the case with small mammals absence of evidence was interpreted as evidence of absence.

This chinchilla rat, now called the Macchu Picchu Chinchilla Rat is said to be arboreal.
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http://www.theguardian.com/environment/2014/sep/26/extinct-cat-sized-chinchilla-found-in-shadows-of-machu-picchu

Genomes show why Hooded and Carrion Crows are different and stay different…and are they different species?

Over the years, as an outsider to the field, I have read about taxonomy and systematics and I have read about different species concepts and the attempts to define what species are. It has struck me that the whole discussion has been concerned with defining the species as a group as opposed to considering the individuals that make up that group. I just have the feeling that defining the group without reference to the individual came from an age when many if not most biologists argued intentionally or unintentionally for group selection with, for example, adaptations ‘important for the survival of the species’ on many lips. As the realisation grew that group selection was the result of flawed reasoning and that the individual is the unit of selection, nobody to me, or at least nobody that I could find, was writing about the species as a collection of individuals subject to natural selection (although this view does seem implicit in the Grants’ work on Galapagos finches). When I did consider the individual I realised that for many organisms, most vertebrates, for example, a species could be defined as those individuals with which an individual could breed to its selective advantage or to put it the other way round, with which an individual could breed without selective disadvantage. Therefore, to me the group—the species— is defined by the advantage it affords its individual members in terms of fitness.

My amateur definition includes those species identified as being completely reproductively isolated (i.e. those that conform to the Biological Species Concept as originally propounded) as well as those, like the Galapagos finches, in which there is gene flow between obviously different species or in which there is a hybrid zone between geographically adjacent forms that differ morphologically and/or behaviourally.  I therefore bridle when I hear only the former referred to as ‘good’ species by those wedded to the Biological Species Concept, with the others left to a ‘judgement call’ as to their status; ‘easily discernible’ should replace ‘good’.

To reiterate, my definition means that complete reproductive isolation (i.e. no gene flow) is not necessary in order to define a species. This definition provides for breeding between neighbouring closely related forms with a hybrid zone between them. If breeding with the other neighbouring form leads to the hybrid offspring having a selective disadvantage then the two forms are retained as distinct species even though introgression occurs.

It is with background that I read a recent paper in Science with great interest. Not only does it throw light on the species problem, it also occurs on my doorstep. The paper, The genomic landscape underlying phenotypic integrity in the face of gene flow in crows, is on the genetic differences between the Hooded Crow and Carrion Crow. It is also interesting not only in its own right but also for the comments it evoked from those trying to decide whether the two crows should be regarded as one or two species.

We live fairly near the hybrid zone between the Hooded and Carrion crows in the West of Scotland. A hybrid lived for several years in the surrounding gardens and school playing field even though it never looked the healthiest of birds and had, what the vets would described as, an ‘unthrifty’ appearance. As well as hybrids, Hooded Crows are reported occasionally since the hybrid zone is narrow at this point and hoodies occur on the islands of Arran and Ailsa Craig where they are said to prefer the higher ground compared with the Carrion Crow.

#487697063 / gettyimages.com

Carrion Crow

#121846129 / gettyimages.com

Hooded Crow


Discussion has centred on whether the new findings offer support to the arguments in favour of considering the two forms as two species, or as subspecies of one species. Over the years they have flitted between being regarded as two species or one. Linnaeus originally described them as two species but throughout the later part of the 20th century, the one species view prevailed with the Hooded Crow listed as a subspecies, Corvus corone cornix, alongside the Carrion Crow, C. c. corone. Then, in 2002 the British Ornithologists’ Union recommended that the two forms should be recognised as separate species (Knox et al 2002). The reasons for this (non-random mating and reduced fitness of the hybrids) and how they fit the Evolutionary Species Concept are explained by Parkin et al  (2003) and by Parkin (2003). Parkin (2003) concludes:

In the case of the crows, I believe that the Hooded and Carrion lineages maintain their separate identities through time and space, for hybrids are at a selective disadvantage. They should be regarded as separate species.

The work that has caused the flurry of interest was done on mainland Europe by Swedish, German and Spanish co-authors (Poelstra et al 2014). They compared Carrion Crows from Spain and Germany with Hooded Crows from Poland and Sweden (as in northern Britain there is a hybrid zone where the two forms meet). The differences detected in the genome and in gene expression have been described and discussed well elsewhere, for example, in a commentary in Science by Peter de Knijff. I will only state here some of the main conclusions.

Differences between the two forms were very small. Only 83 out of 8.4 million DNA positions were found to be fixed and therefore diagnostic of the two forms. As one would expect, the genes concerned were mainly associated with plumage colour. Of the 83 fixed differences 81 were found in a small region of chromosome 18.

de Knijff summed up the conclusions neatly: Poelstra et al. present a unique case of speciation whereby, despite substantial gene flow (especially from hooded crows into German carrion crows), phenotypic divergence likely caused by assortative mating and sexual selection is maintained by genetic variation in less than 1% of the genome. Invoking Darwin on species concepts he concludes: Obviously, forcing complex patterns of biological variation into a single hierarchically structured archive is a purely anthropogenic project. No matter how hard we try, there cannot be a robust, all-inclusive, objective species concept.

While the latter sentence is probably right, I am not sure that the concept of a species is entirely anthropogenic. Defined from the fitness of individuals, an assemblage does have some sort of real existence at an ecological level for example. What I am now convinced is that the Biological Species Concept has had its day in its classical mid-20th century form. It is and perhaps always was too dogmatic; its underlying hypothesis is simplistic and has been undermined by further observations and experiments. Evolution is more complex than that…and continues.

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de Knijff P. 2014. Carrion and hooded crows defeat Linnaeus’s curse. Science 344 1345

Knox AG, Collinson M, Helbig AJ, Parkin DT, Sangster G. 2002. Taxonomic recommendations for British birds. Ibis 144 707–710

Poelstra JW, Vijay N, Bossu CM, Lantz H, Ryll B, Müller I, Baglione V, Unneberg V, Wikelski M, Grabherr MG, Wolf JBW. 2014. The genomic landscape underlying phenotypic integrity in the face of gene flow in crows. Science (20 June 2014) 344 1410-1414

Parkin DT, Collinson M, Helbig AJ, Knox AG, Sangster G. 2003. The taxonomic status of carrion and hooded crows. British Birds 96 274–290

Parkin DT. 2003. Birding and DNA: species for the new millennium. Bird Study 50 223-242

Sitatunga in the Congo Basin

I like antelope. While the tourist safari buses search out lions I look at the antelope, from the ones you can’t miss on the plains to the small ones in the bush. Having been in several places in Africa where we could have seen Sitatunga, swamp dwellers, but didn’t, it was a delight to see one trotting along the far side of the bai as we arrived on the deck of the ‘camp’ (for camp read luxury lodge) at Lango in the Republic of Congo.

The next day we were lucky to see these two males from a boat as we drifted downstream with the engine off. They clearly had their minds on seeing each other off as we came upon them by the side of the river:

The Sitatunga (Tragelaphus spekii) was described in 1863 by John Hanning Speke (1827-1864), explorer of the Nile, but named by Philip Lutley Sclater. Some authors refer to it as T. spekei, I think in what was an attempt to use the modern use of one -i rather than two, -ii. I found this explanation of using one or two:

from http://languagelog.ldc.upenn.edu/nll/?p=1149

I know that the sitatunga is not in the least endangered. I know the economic arguments for permitting hunting by wealthy individuals. But I really find it utterly revolting to find videos on the internet of grown American men and women hunting and killing Sitatunga with crossbows for ‘sport’. What sort of mentality drives such people to make a sitatunga snuff movie?

Ebola: Gorillas and other wild animals

Female gorilla in the Jupiter Group
Ngaga Camp,
Republic of Congo, May 2014
Her toddler was clambering in the trees
above her

The conversation at the funeral of a former colleague with another former colleague, a microbiologist with wide interests who I had not seen for some years, turned to the outbreak of ebola virus (EBOV) in West Africa and how it may spread between wild, domesticated and human mammals, and the characteristics needed for one or more reservoir species, in other words, those that carry but do not suffer to the point of rapid mortality the infectious agent.

In May we were at the site of the 2003 outbreak in the Republic of Congo and heard of the devastating effect ebola had on the Western Lowland Gorilla population. Since returning I have had the chance of catching up with the literature on that outbreak and how it was established that ebola has such a devastating effect on the survival of gorillas, with a mortality rate of 90-95% and the estimated loss of 5000 gorillas from a relatively small area.

Magda Bermejo who lives at the camp in the Republic of Congo we visited (see post of 18 August 2014) after the effective loss of her study groups at Lossi to the ebola outbreak, established the death of gorillas and chimpanzees during human outbreaks, found ebola virus in a number of the carcasses and showed an apparent passage from group to group of gorillas rather than independent transmission form a putative reservoir species. But then, and apart from the enormous potential effect on survival of the great apes in Africa, all sorts of question arise as to who or what becomes infected first and how does the infection (not that easily transmitted according to the evidence with contact through body fluids being needed) pass between groups.

Bushmeat has been implicated as the initial source of human infection while bats, particularly, but also duikers, pigs and domestic dogs are suspected as possible reservoir species. Recently, I see those sequencing the virus collected during the current outbreak have found rapid changes and are reaching different conclusions on the origins of EBOV. The article by Gretchen Vogel in Science (29 August 2014) reads:

Some researchers theorized, based on early sequencing data, that EBOV had circulated for decades, undetected, in animals in the region. But the new analysis, strengthened by the unprecedented number of genomes, supports another theory: that the virus spread, via animal hosts, from Central Africa within the last decade. Researchers aren’t sure which animal to blame, but fruit bats are their leading suspects (Science, 11 April, p. 140). At least one fruit bat species known to carry ebolavirus has a population range that stretches from Central Africa across to Guinea.

That more research on ebola and much more money to fund that research are necessary are truisms. The dangers to those working in a human outbreak to collect samples in areas where facilities for the safe care of patients and basic hygiene are poor also cannot be overestimated. Five of those who collected samples for sequencing  in the current human outbreak have died. Until really hard evidence is obtained from extensive surveys in wild (and domestic) animals over meaningful periods of time and over a wide geographical area, speculation and soft epidemiological evidence may have to suffice in the meantime. But, in that meantime and beyond, alongside local outbreaks that devastate human populations, the great apes of Africa are at risk.

Tom, our former colleague, would I am sure have been delighted that his funeral was the occasion for several coffee-room type discussions on science and science politics; Scottish politicians were not rated highly in the latter.

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Useful starting points for further reading:

Bermejo M et al. Ebola outbreak killed 5000 gorillas. Science 314, 1564
Vogel G. 2014. Are Bats Spreading Ebola Across Sub-Saharan Africa? Science 344, 140
Vogel G. 2014. Genomes reveal start of ebola outbreak. Science 345, 989-990
Walsh PD et al. 2003. Catastrophic ape decline in western equatorial Africa. Nature 422, 611-614
Wittmann TJ et al. 2007. Isolates of Zaire ebolavirus from wild apes reveal genetic lineage and recombinants. Proceedings of the National Academy of Sciences of the USA 104, 17123-17127

Zoology: India gets it wrong again

You really could not make it up. I read in Science (15 August 2014):

India bans dissections
A campaign to bar dissections in India's university classes has scored a major victory. India's University Grants Commission, which sets India's standards for university education, has banned the dissection of animals in zoology and life science university courses. That follows a decision in March by the Medical Council of India to prohibit animal dissection in undergraduate medical courses; it may extend the ban to postgraduate courses. The group People for the Ethical Treatment of Animals has argued that computer models and simulations can replace dissection and that several frog species are now endangered due to large numbers of zoology students collecting them for experiments.

I actually looked at the issue date to check that it was not 1 April. For a country that has made and continues to make bad decisions for the protection of its wildlife I really thought this report was a joke. Future Indian biology and medical students (not, sadly, necessarily the same thing) are to be handicapped for life while the tiger and dhole continue to decline. While in the old (i.e. my) days I argued that the value of dissecting a whole range of invertebrate and vertebrate types was afforded too much importance in schools and universities, I would still regard some dissection as an essential part of being and learning to be a zoologist, medic, dentist or vet (veterinarian, to American readers). In silico and in plastercasto cannot replace the knowledge, experience and sheer nous that will be needed in their future careers gained from handling organs and tissues in freshly killed animals and seeing how and why animals have come to be constructed. With hindsight, I did learn than just the morphology from afternoons spent over a stinking formalin-preserved dogfish digging out the afferent and efferent branchial arteries and the cranial nerves.

Incidentally, to rebut the final point in the report, there is actual evidence that heavy collection of amphibians for laboratory use had no effect on the population*. In search of a soft target, The Unthinking Green religion also forgets the human food trade and the frogs that fill the markets in southern Asia, and the three real causes of the decline in amphibian populations: Overpopulation; Overpopulation; Overpopulation.

I am afraid that India's ban will achieve nothing, other than the perpetuation of ignorance.

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*Cooke AS, Morgan DHW, Swann MJS. 1990. British Herpetological Society Bulletin 33 9-11.

Alfred Leutscher, Wood Mice and the Devil’s Hoofmarks

I have been writing about Alfred Leutscher in one of my other blogs that is covering at the moment the post-war books on the keeping of reptiles and amphibians (http://waicblog.wordpress.com). He wrote Vivarium Life in 1952 and that book which I found on the shelves of the local public library started a burning interest in reptiles and amphibians. The rest is history.

As you can read in the other blog, Alfred Leutscher, a Guide Lecturer at what is now the Natural History Museum in London, was a keen and competent field naturalist as well as a prolific author on the natural world.

While finding out all I could about him, I came across his involvement in a story that has intrigued the world for over 150 years. But before dealing with his role, I need to go back to the early 1960s.

Sometime before early 1963, the BBC televised what I remember as a dramatised documentary on a phenomenon that had been reported in South Devon in 1855—the appearance during the night of mysterious tracks in the snow over a large area of Devon on either side of the Exe estuary that were termed the Devil’s Hoofmarks. Such was the impact of this programme that my friend’s mother thought it unwise of me to travel to Exmouth (one town that was subjected to the phenomenon) for a first visit to my girlfriend’s (now wife’s) then home town. She, the former, not the latter, was really concerned that the devil himself might still be in the vicinity. On and off over the years, I have seen reference to the phenomenon but only when looking up Leutscher recently did I find the whole story.

I am not going to go into any detail here since it is is so well covered elsewhere. In brief, as Mike Dash in the Fortean Times in 1994 and 1996 (combined articles at http://www.mikedash.com/extras/forteana/devil/) put it:

On the night of 8-9 February 1855 (and on one or two nights thereafter trails, resembling those of a donkey, were laid across large areas of Devon. They appeared in shallow snow, between half an inch and four inches deep, meandering through villages and gardens. Sometimes, it was said, they did 'impossible' things, such as crossing roofs, leaping tall walls, disappearing through small holes in hedges, or stopping dead on one side of a haystack, leaving its sides and top undisturbed, and commencing abruptly once, more on the other side.

The newspapers of the day went into full Victorian melodrama mode. Even The Times reported on 16 February:

EXTRAORDINARY OCCURRENCE
     Considerable sensation has been evoked in the towns of Topsham, Lympstone, Exmouth, Teignmouth, and Dawlish, in the south of Devon, in consequence of the discovery of a vast number of foot-tracks of a most strange and mysterious description. The superstitious go so far as to believe that they are the marks of Satan himself; and that great excitement has been produced among all classes may be judged from the fact that the subject has been descanted on from the pulpit.
     It appears that on Thursday night last there was a very heavy fall of snow in the neighbourhood of Exeter and the south of Devon. On the following morning, the inhabitants of the above towns were surprised at discovering the tracks of some strange and mysterious animal, endowed with the power of ubiquity, as the foot-prints were to be seen in all kinds of inaccessible places—on the tops of houses and narrow walls, in gardens and courtyards enclosed by high walls and palings, as well as in open fields. There was hardly a garden in Lympstone where the foot-prints were not observed.
     The track appeared more like that of a biped than a quadruped, and the steps were generally eight inches in advance of each other. The impressions of the feet closely resembled that of a donkey's shoe, and measured from an inch and a half to (in some instances) two and a half inches across. Here and there it appeared as if cloven, but in the generality of the steps the shoe was continuous, and, from the snow in the centre remaining entire, merely showing the outer crest of the foot, it must have been convex.
     The creature seems to have approached the doors of several houses and then to have retreated, but no one has been able to discover the standing or resting point of this mysterious visitor. On Sunday last the Rev. Mr. Musgrave alluded to the subject in his sermon, and suggested the possibility of the foot-prints being those of a kangaroo; but this could scarcely have been the case, as they were found on both sides of the estuary of the Exe.
     At present it remains a mystery, and many superstitious people in the above towns are actually afraid to go outside their doors after night.

The ‘mystery’ has continued to fuel speculation over the years with explanations ranging, as might be expected, from the supernatural  and cryptozoological to the zoological and the meteorological.

David Sealy in an article in The Skeptical Intelligencer (6, 12-19, 2003) explained how Alfred Leutscher became involved in providing an explanation for what had been seen:

The late Alfred Leutscher was, in 1964, senior Guide Lecturer at the British Museum (Natural History), South Kensington, now called the Natural History Museum. He was interested in many things, and was an acknowledged expert on animal tracks in snow, of which he had a large collection of photographs. In that year he published, in the wildlife magazine Animals (now sadly defunct)[It became BBC Wildlife, notable for many years for its Unthinking Green religious agenda] an illustrated article (Tell-tale Tracks: vol.3 no.11, pp.297–299) on the subject. At the time he had never heard about the ‘Devil’s hoof marks’. I was then a relatively junior curator in the Palaeontology (fossils) department, but on seeing Leutscher’s article I dared to draw the great man’s attention to Gould’s book. The response was immediate: he quickly identified the tracks as those of the common nocturnal wood mouse Apodemus sylvaticus (hundreds of them), hopping across the unaccustomed snow, and published photographs (1965: The Devil’s Hoof-marks: Animals, vol.6 no.8, pp.208–209) proving the point. He also addressed the Zoological Society of London on the theory… Leutscher wrote: Other trails which are made in a straight line are those of an animal which hops. All four feet land in a bunch, in a leap-frog action, so that the hind tracks are leading. When this happens in a soft medium like snow, especially when it begins to melt, the tracks become blurred and run together. The result is a ‘U’ or ‘V-shaped’ impression. Examples of such leap-frog hoppers among British animals are the hare, rabbit, squirrel, rat, and mouse.
     The drawing submitted by ‘South Devon’ shows a trail of clear hoof prints, each an exact facsimile, as if made by some tiny animal whose feet were shod. Such clear and regular prints seldom occur, since irregularities in the ground or snow cause variations in size and shape. One is tempted to think that the observer in this instance did not draw what he actually saw, but rather what he wanted to see – the hoof-marks of Satan. This is understandable, since a common human failing in most of us is to let a preconceived notion mar our judgement.
     Another drawing which I examined, by a correspondent signed ‘GMM’, has given me a clue to a possible solution to this mystery. It shows a carefully drawn set of tracks, each of irregular shape, and roughly ‘V-shaped’ in contour. This is precisely what a small hopping animal would produce in snow, and there is only one British animal small enough to fit the Devon trails – the wood mouse (Apodemus sylvaticus).
     It was during a search for snow tracks in Epping Forest, in the severe winter of 1962– 3, that I came across dozens of trails of the wood mouse, each consisting of small ‘V- shaped’ marks regularly spaced out and conforming to the measurements which were given a hundred years ago. When I found them I was totally unaware of their significance (Animals, 18th February 1964).

In the intense cold and silence of the forest, what could have been a better setting for the return of the mysterious Devon visitor. In this case, however, the mischievous little rodents were playing the Devil at his own game!

from David Sealy's article, Trailing the Devil, Skeptical Intelligencer 6, page 15

A number of writers have continued to treat the phenomenon as a ‘cryptozoological’ mystery, to the annoyance of those who argue that Leutscher had provided an explanation. Some questioned, reasonably, why on that (or those) particular night(s)? Here is Mike Dash (who gathered all the original reports into one convenient publication):

There are, nevertheless, drawbacks to the rodent theory. Proponents have to explain why large numbers of mice or rats hopped such very long distances, rather than walking or scurrying about, thus leaving a more readily identifiable mixed trail. There must also be some doubt whether a single mouse or rat could really cover the distance of almost five miles (from Dawlish churchyard to Luscombe, Dawlishwater and then Oaklands which one party claimed to have traversed in following a single trail. And while it would seem possible for rodents to climb onto roofs, there seems no good reason why they should want to hop so singlemindedly over them. Finally, rats and mice are so common that one would expect trails similar to the Devon marks to be reported far more frequently than they actually are.

All of these ‘drawbacks’ do not seem much of a problem to me. Indeed some can be broken down to testable hypotheses. Leutscher had already shown how the marks are formed as snow melts after a fall and the ability to be fooled by footmarks in melting snow as the impression enlarges and changes is well known. The long single trails can be dismissed if many different animals were involved with observers simply moving one and then spotting another. Do Wood Mice (better known to those of us of a certain age as Long-tailed Field Mice) hop rather than walk in snow of a certain depth (as one might expect)? It is entirely plausible that the mouse population had reached a periodic high in 1855 and they were, after snow, desperate for food and hence highly active. So were those nights in 1855 a combination of circumstances: a large population after a boom year; a depth of snow that encouraged leaping and melting snow the next morning that created the distinctive appearance of the tracks? Add to that a superstitious human population amplifying, distorting and simply misinterpreting observations, aided no doubt by the intake of a pint or three of scrumpy, you have, in my opinion the ideal mixture to fuel an everlasting ‘mystery’ story. But eventually along comes to Alfred Leutscher who provides a rational explanation to the 1855 phenomenon.

But rational explantations are not welcomed by some individuals and still the discussion rumbles on in websites run by mystics, without even a mention of Leutscher’s interpretation from evidence firmly based on his knowledge gained as a field naturalist.

Finally, a couple of camera trap photographs from the bottom of our garden. When we next get snow (an uncommon occurrence here) I shall be watching t see what tracks they leave.