Showing posts with label systematics. Show all posts
Showing posts with label systematics. Show all posts

Tuesday, 19 November 2019

Chinese Giant Salamanders: How many species are there?

Two well-publicised papers, published in 2018 and 2019, based on analysis of mitochondrial and nuclear genes, propagate the view that there is more than one species of giant salamander in China, that these species are ‘cryptic’ in that they do not differ in appearance, and that some are in imminent danger of extinction through ignorance of their existence. The authors certainly established that there are a number of distinct genetic lineages of giant salamander in China, enough to convince adherents to the phylogenetic species concept that they constitute different species. However, whether they are ‘good’ biological species is a matter that can be debated endlessly.

Giant salamanders in China in the wild are endangered because of over-collecting for the human food trade and from loss of habitat. Those working on the origins, evolution and conservation of these animals face major difficulties. The escape or release of wild-caught and farmed animals transported alive in large numbers throughout China in recent decades means that the geographical origin of newly-collected specimens cannot be guaranteed. By using specimens in museums collected before the vast increase in trade, the authors of the 2019 paper have overcome this problem but at a cost; the number of available specimens was small—just 17 individuals—since the DNA of many early specimens had been degraded by preservation in formalin.

The lineages are associated with the mountain ranges formed during the great geological upheavals that formed the Tibetan plateau starting about 3.3 million years ago. The authors of the 2019 paper realised that two of the lineages could be attributed to species that had been named in the past.

One lineage was be attributed to the classical domain of the Chinese giant salamander—in the northern Yangtze/Sichuan region—and conforms with Andrias davidianus. A second lineage from the Pearl River tributaries in the Nanling Mountains of south-eastern China appears to be that described by Edward George Boulenger in 1924 as a separate species, Andrias sligoi, that was later lumped into A. davidianus. A third lineage from the Huangshan mountains of north-eastern China has never been described as a separate form previously and could be a new, as yet un-named, species.

Boulenger noted morphological differences between what he named Megalobatrachus (now Andrias) sligoi and M. maximus. He would, wouldn’t he, since that is how new species were described then. But just as at the present with molecular genetic data, different people in the trade regarded some differences as too small to justify separation into a new species; others regarded the tiniest difference sufficient.

At that time Boulenger took his father's (George Albert Boulenger) view that any observable differences between Chinese and Japanese giant salamanders were too small to consider them as two species and continued to lump them into one, M. maximus. While he could find no consistent difference between the Chinese and Japanese forms, others claimed they could and the species maximus was split again into the Chinese, davidianus, and the Japanese, japonicus.

Ignoring the arrangement of tubercles on the head (which appear to differ somewhat in the Chinese and Japanese species) Boulenger also differentiated sligoi by its longer, flatter, and smoother head, and by the shorter distance between the eye and lip.

How Boulenger distinguished his new species, M. sligoi

Boulenger’s new species did not survive as such. Later authors argued it was no different or insufficiently different from davidianus and into the latter it was lumped. Liu in his Amphibians of Western China, published in 1950, condemned Boulenger’s erection of sligoi as a separate species:

Neither the length of the head (which is difficult to define, and which was not defined by Boulenger) nor the relative distance of the eye from the labial border are valid characters.

But Liu did not say why the characters are not valid!

We therefore seem to have agreement between morphology (whether declared ‘valid characters’ or not) and molecular genetics published 95 years later. However, I too have doubts about Boulenger's comparison (see later article). But Boulenger may have been right all along, and the name given recently, South China Giant Salamander, Andrias sligoi, an appropriate one. However, that is only if you agree that species should be defined in that way and not by the biological species concept.

Before accepting the increased number of proposed giant salamander species, perhaps it is worth considering whether the results of the recent artificial mixing up of lineages in both China and Japan (A. davidianus has been released into Japan) have not already invalidated that proposal.

‘Good’ biological species do not or only rarely interbreed in the wild. The classic difficulty with deciding whether species whose ranges do not overlap (i.e. they are allopatric) are ‘good; biological species, is that they do not meet in the wild, and the question of if, say, a geographical barrier were to be removed, would they interbreed naturally, cannot be answered. However, if lineages interbreed freely after translocation, then the case for their being biological species is severely dented if not holed beneath the waterline. Indeed, in the 2018 paper, the authors, do show that hybridisation between lineages has occurred in farms. Similarly, hybridisation between Chinese and Japanese forms has occurred in Japan where the former has been introduced.

On the evidence of hybridisation, then, the case for a number of ‘good’ species of giant salamander, according to the biological species concept, is weak.

The authors of the two papers (many of the authors are common to both) are concerned, rightly, with the conservation of giant salamanders and with the measures that should be taken to ensure their survival in the wild. However, the type of evidence used—that different lineages equal different species—is clearly not acceptable to adherents of the biological species concept. Indeed, if it that premise were correct, two of my daughters-in-law would be of a different species to me and my grandchildren interspecific hybrids. Thus, Jerry Coyne, a world authority on speciation from the University of Chicago, in his blog, Why Evolution is True, wrote:

…virtually every paper I’ve seen on the process of speciation—that is, on the ways that new species come into being—deals not with the accumulation of genetic distance per se, but on the development of reproductive barriers that eventually prevent populations from exchanging genes.

Greg Mayer of the University of Wisconsin, making the same general point from a different case on Coyne’s website:

…At the time, this bothered me, as I saw it as an application of the old morphological species concept, extended to genetic data: if you can tell them apart, they are different species. This is also what Jerry argued against… an arbitrary amount of morphological or genetic difference, or inferred time of separation based on the amount of genetic difference, is not a sound basis for a species concept.

Here, sadly, there may be incompatibility between the politics of conservation and science. Conservationists find it easier to provoke politicians into action with measures to protect species rather than populations and habitats—thus the more species, the better the argument and the greater geographical spread of habitat protection.  However, Jerry Coyne has argued cogently:

…the ‘splitting’ of species [in this case discussing the Giraffe, ‘split’ into different ‘species’ by virtue of differences in genetic lineage] is a conservationist motivation, not an attempt to partition out nature in biologically and evolutionary meaningful ways’.

The research on the giant salamanders reminds us of some fundamental biological questions, like the perpetual problem of how we define a species, as well as some urgent practical conservation concerns. Indeed the research highlights the urgent need to protect, manage and re-introduce populations of giant salamanders in the wild.

However we regard Boulenger’s Megalobatrachus (now Andrias) sligoi, the discovery of his type specimen is an interesting story that I will cover in a further article…and can we determine where those giant salamanders used for class dissection in Hong Kong in the 1960s came from?


Boulenger EG.. 1924. On a new giant salamander, living in the Society’s gardens. Proceedings of the Zoological Society of London, 1924, 173–174 

Turvey ST, Marr MM, Barnes I, Brace S, Tapley B, Murphy RW, Zhao E, Cunnigham AA. 2019. Historical museum collections clarify the evolutionary history of cryptic species radiation in the world’s largest amphibians. Ecology and Evolution 2019;00:1–15. https://doi.org/10.1002/ece3.5257

Yan F, Lü,J, Zhang B, Yuan Z, Zhao H, Huang S, Wei G, Mi X, Zou D, Xu W, Chen S, Wang J, Xie F, Wu M, Xiao H, Liang Z, Jin J, Wu S, Xue C, Tapley B, Turvey ST, Papenfuss TJ, Cunningham AA, Murphy RW, Zhang Y, Che J. 2018. The Chinese giant salamander exemplifies the hidden extinction of cryptic species. Current Biology, 28, R590–R592. https://doi. org/10.1016/j.cub.2018.04.004 


Sunday, 28 September 2014

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.



Carrion Crow




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.

---------

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