Morphological taxonomy is the first requirement. Without classical taxonomy it is impossible to carry out molecular Taxonomy I(it is like a Tyre you donot know which car it belongs to) . That correct identification is done by morphological characters and then the specimen is borcoded and the borcode is submitted. If some one identifying based on barcode which is present in BOLD / gene bank and the one who has submitted has missed correct identification, the exercise goes wrong. Therefore it is requested to go far correct identification seriously then only bar code and submit. If I have identified a specimen correctly and I try to match bar code of my specimen with already present in BOLD/ genebank, is wrong then I will land with many confusions like I will think mine is a new species etc. IT HAS TO BE DONE VERY CAREFULLY.

That depends on your task. If you want to identify known species that are morphologically well differentiatiate, then, yes, morphology alone is more than enough.

If you want to delineate 'new' species that are morphologically not clearly demarkated, then DNA is a great tool. For eaxple, in the case of a crustacean that we could not differentiate into morphological species a priori, we were able to show that it constited of two reprodcutively isolated species that occured in sympatry. Having each single individual assigned to a 'DNA species' we were eventually able to find some morphological characters as well to separate them (due to the overall plasticity of the markers this had been impossible without the DNA data).

Also, whether morphology (or DNA) is enough depents heavily on your species concept. To delineate species based on the Biological Species Concept you may need more than some morphological differences (or more than some DNA information...). You can look at the following paper for details:

http://onlinelibrary.wiley.com/doi/10.1111/j.1095-8312.2011.01746.x/full

Thanks, but it’s known that percent DNA sequence difference is different in different taxa. Intra- and interspecific sequence divergences is widely variable. There is no standard percent sequence divergence known, therefore it would be very hard to judge, whether you have good species or this is morphotype of same species in different taxa.

Definetely! Sequence divergence alone does not allow the differentiaiton of species (as it is done in some applications of DNA barcoding). But if you use two or more independent markers (e.g. one mitochondrial and one nuclear marker; or one DNA and one or a set or morphological markers), and both consistently result in the same lineages (or clusters or groups) of individuals, these lineages may be different species, at least if they occur in sympatry (and if you care about reproduction as the defining criterion for species). In this case, these lineages obviously did not reproduce, although that had the chance (sympatry). If they occur in allopatry no unambigious conclusion can be drawn. But the same problem would arise for morphological differences between geographically separated species/morphotypes. The problem is: in most cases, people do not specify what species concept underlies they conclusions regarding the the differenciation of species.

Bear in mind too George that, occassionally, species that appear to be morphologically distinct demonstrate limited sequence divergence. That's what we found when we looked at 'species' of fruit bat on islands in the Indian Ocean: https://www.researchgate.net/publication/24144045_Multiple_colonisations_of_the_western_Indian_Ocean_by_Pteropus_fruit_bats_(Megachiroptera_Pteropodidae)_the_furthest_islands_were_colonised_first?ev=prf_pub

Article Multiple colonisations of the Western Indian Ocean by Pterop...

I am a great fan of traditional morphology.

But in some cases, pure morphology can bring incorrect results.

For example, when you have species with different ecotypes.

Then you have the problem , that "species that appear to be morphologically distinct demonstrate limited sequence divergence" (as John said).

In some other cases,some morphological characters can be absent (because of damage,...) so you cannot determine the exemplar. Then you need dna.

I worked with Ziphhidae, their skulls are a challenge.

Morhology adds to the evidence that you're dealing with separate species. But so does DNA, as well as differences in ecology, in behaviour, in whatever you name. DNA can help to discover cryptic species, which are not recognisable from morphology alone....

If you want to read more: http://onlinelibrary.wiley.com/doi/10.1111/j.1756-1051.2013.00158.x/abstract Although written with apomicts in mind, it has value for other groups too, I think!

I do not agree that DNA is useless. These days i am working on DNA barcoding of scorpions of Pakistan. In most of the cases morphology is sufficient. But some time member of two species are are very similar phonologically but their DNA sequences are totally different. DNA sequences are very helpful for cryptic species.

Muhammad: I fully agree with your comment, as stated above already!

Of course, we should all present as much evidence as possible to support any claim we make in a study - whether that means clumping together or splitting 'species'. So, if you have the opportunity, the skill and the means to carry out both morphological and genetic work (or other methods), then you should do so. If the results of both methods agree, great, and if they don't, well that's another interesting paper!

An African lion is an African lion, no? What about Timbavati White lions (incipient species, sub-species, breed, genetic anomaly)? We are not able to delineate all species so clearly and I very much doubt there will ever be a clear-cut "definition" of a species, so restricting ourselves to one line of evidence is misleading - that probably would not stand up in a court of law! Taxonomy evolves on the basis of consensus - between scientists and between fields of research; the more all-encompassing our research is, the easier it is to find consensus.

I think that they complete each other they are in a circle. You need to identify wasps by morphology, to classify them to extract their DNA then to submit it in the Genbank . For non taxonomist , they only have to amplify a specific gene and to blast sequences to identify their wasps but only if there is a good database in Genbank of all species in the world. Otherwise using molecular tools will be hard to do! So we need both morphological and molecular work!

This is a very interesting topic and I really want to give you two examples of how morphology can be useless (sometimes because taxonomists are not necessary agreed on certain features). This is the case in some Afrotropical butterflies, where one author synonimised or treated some species as synonimes of another species in his work, while the other accepted the minor differences between the two (or even three species) treating them as "good" species. Now, I was lucky to found caterpillars of three species in the group and I could also rear them to butterflies. Two of them actually co-occur in West Africa and they have morphologically completely different larvae and pupae! When the butterflies hatch, you can still check the minor moprhological difference on the imagos, which were consistent on the two species. So in this case, the answer was there in the morphology, but some taxonomists do not look further than the imago stage..(the third species has a different looking caterpillar as well). In this case, DNA barcoding could have shown us the specific differences through gathering enough information from various populations, solving the taxonomic debate (my breeding data unfortunately is still unpublished).

In another example, for a long time an Afro-tropical pierid butterfly was believed to be monotypic in the sub-family Pseudopontiinae. It was only an extensive DNA study revelaled that actually multiple species are involved in a complex, where there were no or very little morphological differences were found (in the imago stage). The study was published here: http://onlinelibrary.wiley.com/doi/10.1111/j.1365-3113.2010.00549.x/abstract;jsessionid=7F0C49F1A5082F2231E02B7EC3650F4C.f01t04?deniedAccessCustomisedMessage=&userIsAuthenticated=false

but actually publishing the paper raised further debates on the specific status of the newly described species, as other taxonomists stated that in this case we were supposed to tread the taxa as subspecies. Obviously, they had no experience in Afro-tropical bio-geography and the biogeographical barriers, but still, this forced me to collect more evidence on the specific status of Pseudopontia gola, which I have found in the pre-imaginal stages (again). The larva and the pupa turned out to be morphologically so different from the Central-Southern-African P. zambezi, that they obviousy cannot belong to the same species (the description of the pre-imaginal stages of P. gola was just submitted for publication).

So as you can see taxonomy is so complicated sometimes and there are cases, where firm evidences could not be found easily. In these case DNA could be very useful, while in other cases, morphology could be looked at even in the pre-imaginal stages!!!

Hope you find this answer useful!

Best wishes

Safi

To me both morphology and DNA are tools. Both can and should be used. I think morphological approaches still have some distinct advantages as with this dataset you can bring in fossil taxa, which I think always makes for interesting results. However, it is also true that DNA can be very useful in working out the relationships of cryptic species, ie more or less identical species that are actually not related. One case of this that I was involved in was Myuchelys georgesi and Flaviemys purvisi. Very similar turtles that are not even closely related. But again they are both tools and should be used together and also with other datasets too.

"DNA data is useless unless you don't know the exact species name."

I think this part of the (quite confusingly phrased) question refers to DNA barcoding which does not equal taxonomy.

I agree that DNA barcoding is not alternative to traditional Taxonomy but we can say that DNA barcoding is a tool which is helping Taxonomists even non-taxonomists to quickly identifying species using existing information of gene sequencie in the gene bank. Instead to DNA barcoding scientists are using DNA base taxonoly for phylogenetics studies. I think even for identification of species instead of using only 652 base pairs of CO1 (DNA barcoding) we should also involve other genes to get more insight. But it should be done for cases where one is not able to identify the species morphologically as it is much technology. We found that 12S, 16S (mitochondrial genes) and 18S and 28S (nuclear genes) are also very important.

Fortunately, the molecular techniques are rapidly getting cheaper and cheaper right now. However, we should be careful not to rely exclusively on DNA just because it will soon become very convenient and easy. As said before, DNA sequencing is just one of the tools that help in resolving phylogenetic relationships between taxa. It can be misleading on its own.

I am agree with to all researchers suggestions.

DNA is a main genetically molecular of species organisms . If you are know to species through the morphological characters than after we goes to DNA level. DNA Barcoding is the best process to identify the second sample of the species to anywhere.

Morphology-based keys support accurate identification of many taxa. However, for taxa

that are not well studied, or for which distinguishing morphological characters have not been discerned, identification can be difficult. Accurate identification is especially problematic for very small organisms, for members of cryptic species complexes, for eggs, and for immature stages. For such cases, DNA barcodes may provide diagnostic characters. The correct identification of species is essential to the performance of ecological and evolutionary research.

I think even a barcode is not sufficient for accurate identification of many species and we may require support of other genes like 12S, 16S (mitochondrial) and 28S and 18S (Nuclear)

Dear All,

It depends on the taxa. Regarding insects, in most cases traditional morphology based taxonomy is sufficient. I stress one should identify individuals in huge numbers and many of them are dead at the moment of identification.

Using molecular biological tools in identification is too expensive, too complicated and needs a sophisticated laboratory.

However, cheep and in large number usable molecular biological methods could help to identify sibling species which are different to identify morphologically.

If the taxon is not well studied morphologically, if there is no genbank data for less studied or well studied taxa sufficiently. How can DNA methodology help? It can just say difference or closeness (even this is not much help, because of many reasons) to each other. It can't say species belonging. I do think that we must also take in consideration, who did DNA work and who uploaded information in Genbank. I agree with Mukesh Mali, It's good for second sample of the species. :-)

I don't think that morphology provides all necessary data to define a species. At least not at fungi, bacteria and other microorganisms and in cases which Pir Ali has mentioned: "Accurate identification is especially problematic for very small organisms, for members of cryptic species complexes, for eggs, and for immature stages."

Molecular methods of identification of species are important for example in phytosanitary laboratory, where they need to identify a pest in a sample, taken from a consignement in international trade. The method should be accurate, fast and not too expensive. Of course the method is developed based on genom (or a defined sequence) of known species. Actually a good diagnostic protocol should be developed. For plant health official labs diagnostic protocols are developed under the umbrella of EPPO:

http://www.scoop.it/t/diagnostic-for-pests

Best regards,

Vlasta

For taxa where accessing DNA is a possibility, morphology is generally sufficient to define a species, but DNA can greatly help and in some cases in invaluable. In my work on diverse invertebrate groups from coral reefs, I use DNA and morphology as two lines of evidence that will either support or refute that hypothesis that two specimens belong to the same species. In some cases, the genetics show that something more complicated is going on (reproductive isolation or hybridization for example), in other cases, the DNA evidence supports the relationships suggested by morphology and make a more convincing argument when providing an identification. Morphology, DNA, behavior are all characters of a species that can be drawn on to understand a species.

Once you understand the system you are working with, morphology is often enough to easily and accurately ID taxa, but ignoring the information that a DNA holds is similar to putting all your weight on IDs based on shape and disregarding color when it may be a useful character.

I think DNA data are very valuable, and sometimes help you to decide. Now, it is still not the time to define species solely on the molecular characters (at least in my field - aquatic beetles), but in combination with morphology they are very helpful. On the other hand, there were described species, using morphological characters, and now, based on new molecular data it was shown, that the differences were due to infraspecific variability.

In insects, distinguishing species began with superficial physiological differences. Then came the discovery that the genital armature varies, and this helped identify many 'cryptic' species; now along comes DNA data, which is again very useful. However, it is not one or the other that is superior, it depends on the taxa being studied. I feel that the most important requirement in taxonomy is common sense, so that, lacking a universally acceptable definition of species, one can separate taxa with reasonable certainty using various criteria. Like any tools of any trade, it is the way they are used that is important. In the hands of a master, a saw and a hammer can build a house; in the hands of an incompetent, they can result in amputations and swollen thumbs!

An example where DNA can help is when dealing with animal parts - e.g. dried shark fins. DNA barcoding has been shown to be able to accurately distinguish 99% of samples of sharks and rays to species. When dealing with dried shark fins where morphology of fins is difficult, DNA barcoding provides a method for determining species composition which was previously lacking. So yes, in some cases DNA is very useful for taxonomy. It is a tool and like all tools it can be misused and a lot of people do/have misused this tool. But in the right hands it is a powerful tool which should not be ignored, but instead used in concert with classical taxonomic methods.

I am assuming that by taxonomy you meant the description of species. In my view, both of the techniques compliment each other. Is (comparative) morphology insufficient to describe species? Yes. There are cases where comparative morphology has its limitations. For instance, in the case of sibling species, members of two or more species groups are morphologically indistinguishable but are basically different species (based on, for example, reproductive isolation). In this case, other studies (if possible) such as barcoding (based on the assumption that particular gene sequences are varying in the sibling species) can help to identify species differences that are not visible morphologically. So DNA based studies can supplement morphological studies when it comes to describing species. Furthermore, once a barcode has been assigned to a valid species, future researchers, if it is convenient to them, need not utilize traditional methods of species identification. Rather, they can simply find out the barcode sequence for their specimen and compare it with the available data to get an ID (though, I fear that the actual situation might not be so simple). So now we arrive at the second point, is DNA data useless, unless one does not know the exact species to which it belongs? Yes I agree with you. Suppose you get a DNA barcode sequence of a known reliable marker of your study specimen. You are absolutely sure that its something new because that sequence is not already reported. The trouble is, in order to describe a new species, you will have to go to the traditional taxonomic procedures (as dictated by, for instance, the ICZN for animals) which again highlights the fact that a departure from traditional taxonomic procedures is not possible. Furthermore, even if your barcode matches with a known sequence, I would say that one will have to consult a traditional taxonomist to be sure about the conclusion. As a concluding point, I want to add that many groups of animals (other organisms as well) have stable taxonomies based on morphological characters. Those who work in the area know that morphology is often quite convincing when describing species differences.

The best solution for this taxonomic troublesomes is supplied by the integrative taxonomy point of view. Thus, alpha taxonomy should be complemented by means of other technical tools, as those supplied  by electron microscopy, geometric morphology, euclidean morphometry (mulivariate analysis), cytogenetic, molecular tools.

I work on biodiversity in tropical rain forests. The tens of thousands of species are--and have to be--defined by morphology. To make sense of the environment and to manage it, we will always need to identify things by eye and hand lens, not by molecular analysis. Cryptic species are discovered within morphological species--they cannot be discovered nor explained independently.

There is a bigger problem at the level of higher taxa where the molecular data can be completely unsupported by morphological data, for example the placement of Rafflesia in Euphorbiaceae. Are we supposed to accept the molecular analysis and ignore the total lack of morphological linkages upon which our ideas of relationship have historically been based?

Here is one of latest papers which highlights how DNA barcoding can be very misleading. But more detailed genetic analyses, particularly including nuclear exon data, combined with morphological examination managed to resolve this 'complex' of chimaeras despite huge discordance between mtDNA and morphological data. Using DNA barcoding to support species delineation is valid; using it without or with lack of morphological data is bad science and helps no one except the author obtain another paper

In the Abstract of Dr. William`s paper about Chimaera ogilbyi is indicated: " An integrated taxonomic approach..."; THIS SHOULD BE THE SOLUTION TO THE TAXONOMY DILEMMA IN DISCUSSION: INTEGRATIVE TAXONOMY!!!

Completely agree Dalmiro - an integrated approach is the only way to go. Only way you will find discordance. Understanding where we have discordance will lead to research in future which can properly explain why we are getting that discordance rather than just sweeping it under the rug

Dear William

Thank you very much for your comment. Unfortunately nowadays many Ecologists and Biodiversity specialists are trying to use DNA approaches without any Morphological support. They try to identify diversity of species, however I don't see any reason to do this without knowing what species we are dealing with. Therefore I completely agree with you and Dalmiro, that DNA must be used in combination with Morphology and this messages must be sent, very frequently, to all scientists dealing with DNA taxonomy and DNA use in Biodiversity.

Dear George,

I completely agree, but I do feel that we are now finding where some of these DNA approaches without morphological support are wrong so I am hoping this might start to concern people and force them away from that approach. Unfortunately the plethora of journals available these days means even the worst science can get published somewhere. That is a worrying trend

DNA based approach in taxonomy has been established as a fascinating subject. Currently these methods are used to differentiate cryptic groups and closely related groups. Further, the younger researchers prefers to do identification based on DNA based rather than morphological based. Even the commercially available easily recognizable known species also DNA based studies are alarmingly used. It could be avoided and in my view, this methods could only support the conventional taxonomy. As highlighted earlier by the learned, conventional taxonomy has its own merit and could be used at field level and requires no additional time. So, I support strengthening of morphological based identification .

Morphological taxonomy is the first requirement. Without classical taxonomy it is impossible to carry out molecular Taxonomy I(it is like a Tyre you donot know which car it belongs to) . That correct identification is done by morphological characters and then the specimen is borcoded and the borcode is submitted. If some one identifying based on barcode which is present in BOLD / gene bank and the one who has submitted has missed correct identification, the exercise goes wrong. Therefore it is requested to go far correct identification seriously then only bar code and submit. If I have identified a specimen correctly and I try to match bar code of my specimen with already present in BOLD/ genebank, is wrong then I will land with many confusions like I will think mine is a new species etc. IT HAS TO BE DONE VERY CAREFULLY.

Dr. Jaiswar. I am fully in agreement with your sentence...

Dear George,

I completely agree with Will's statements. Please find attached a paper published in 2017. It includes a discussion on taxonomy based on morphology, morphometrics and meristics vs. molecular taxonomy. As pointed out in that paper, a combination of genetic and morphological-skeletal results, incorporating morphometric and meristic evidence, should be considered ideal in my opinion.

Best wishes

Simon

In my opinion molecular taxonomy does not exist without morphological or classical taxonomy . molecular tools help you to differentiate the species where you are not able to do that with external morphological characters. Most of the cases hard parts are able to clear these type of ambiguity too. Any body who is bar coding a species without identification using morphological characters should be care full, one may land up in wrong identification.

Unfortunately all tools can be misused, but morphology is under selection and can be misleading with regards to speciation, especially in the presence of crypsis. Too much emphasis is placed on morphology because for so long it was the only tool available, and yet, it can and has been used subjectively to reinforce people's opinions over objective data (plus, the fact that some taxonomists refuse to even collect tissue samples on the basis that genetics is a false science is just absurd). Genetics is more objective, so as a tool, when used properly, is very useful to use with other tools that are more subjective. Some more traditional scientists seem to be anti-genetics because they don't understand it, but neutral phylogenies remove the subjectivism from morphology when used properly. WHEN USED PROPERLY. Like all tools, including morphological ones! The more tools the better, because as Will said, you're more likely to find cool stuff that way. There are no bad tools, just bad scientists.

A bit left field I know but this conversation got me thinking. As someone not working on taxonomy (genetic or classic) and not fully across the field I wonder what the prevailing thoughts are on using eDNA to measure biodiversity and the presence/ absence of a particular species in an ecosystem?

In the field of pseudoscorpion studies, where they show massive variation in morphology based on location, molecular work helps a lot.

Morphology doesn't always reflect taxonomy : as T. Daly-Engel said, it can be under natural selection pressure, and therefore, a similar ecological pressure can lead to similar morphology, which doesn't necessarily reflects a relationship, and today is supposed to be phylogenetic : Müllerian mimicry is one example.

Morphology also isn't always selected : it can be due to genetic drift, for example, and on the other hand, a morphological split not always reflect a taxon split.

As many morphological critters have been used in the past, some proven useful, other treacherous, how to know a morphological difference reflects or not a taxonomic difference ?

Whatever definition of the species is taken, it always largely relies on the notion of reproductive isolation, which is supposed to lead to genetic isolation : therefore, genetically close but morphological different forms don't necessary belong to different taxons. On the other side, genetically different, similar looking forms might set trouble...

Of course, it depends on the genetic material examined : not all genetical sequences, as not all morphological features, are good to lead to strong taxonomics.

I find both methods to be interdependent and indispensable. The use of DNA, is a contemporary tool, being used by scientists to verify their findings. We need to quickly realize and accept the technological evolution happening in the science field at the same time we should not denigrate the yesteryear tools which were used in species identification.

Thanks to all, for your very interesting and professional answers.

Well, now let's think, we know names only for 1.2 million Insects, but most realistic estimated number is between 3 to 8 million. Therefore we know only 15-40% of existed species of insects, but we have no idea about rest. Also, if we check already known species, huge number of species known has no any perspective to be sequences, as most of types are either destroyed or in very poor condition, therefore we can't use them too. So, now we have DNA tools and we can identify, name and even place the species in taxonomic order, but if we have no knowledge of their morphology, how can it be useful for practical use? I mean to measure diversity or use in bio-control?

taxonomy based in morphology will never disappear and is essential, as with any "tests" one can only find what one is looking for, therefore in terms of order, morphology should come first and molecular analyses in its wake. Molecular has given biologists an incredible tool to refine and elucidate difficult cases and will continue to do so. But, one has to bear in mind that these technological advances are the result of policies, development programs, funding and the like, that have been promoting over the years (last 30 years) the use of these tools, and our bean-counters and policy makers are rejoicing because at last they can assign a finite reference to species as an invariable unit, or are under the false impression that they can, forgetting completely the elasticity and variability surrounding what constitute a species, the famous species concept and the fact that science, readily and necessarily embarrasses these variabilities.

This to say that today's urge and insistence to use these "technologies" over "traditional" methods is not just the result of a genuine scientific need, but also that of an administrative process emanating from technocrats and policy makers, filtered through mass-media and becoming a societal need (?).

I would say a big YES for for question, if it is attempted properly.

Classical taxonomy is the base so we can't ignore its importance but for confirmation we can go for molecular taxonomy or tools

Isn't DNA a form of morphology as well? It is just that DNA is structure at the molecular level. Whereas the morphology we are referring to is mostly gross morphology. I would say they complement and supplement each other. Both are in a sense morphology but at different scales.

I would like to add that DNA, gross morphology are all characters of a species. These need to convey consistent messages and if possible their meanings should concur with each other.

Identification of closely related species, Identification DNA-based is beneficial even though anatomical and morphological information is still very much needed. I experienced this case in some fish from the coral reef ecosystem.

Classical taxonomy is the basis for identification of any species but the ambiguities can be resolved using DNA barcoding. Presently many of the barcodes are too ambigious so precise and punctuated efforts together with classical and DNA BARCODING is a solution to understand the diversity of life

Ever heard of NCBI BLAST?

Certainly DNA helps a taxonomy. This is extremely helpful in identifying very closely related species. Diagnostic or key characters can be combined with DNA barcoding for the identification of them. This way, we confirmed identification of Ompok pabda to separate from Ompok bimaculatus (Siluriformes)

I think that molecular data is helpful method to confirm and complete the morphological

identifican of any specimen, as well as it could provide essential information about distribution of species by doning compartments between DNA barcodes.

in my opinions morphological analysis is the first method to used for animal or plant species identification, but sometimes when we had problem with the species that have similar morphology characteristics. We can use DNA analysis like barcoding to helpful the identification analysis.

What happens with DNA results and all other forms of data, i.e. morphology, ecology, behavior, biogeography appear to be in serious conflict? In pinnipeds, DNA results argue for monophyly, whereas all other data appear to support Diphyly.

Genetic diversity has been measured incidentally and inferentially through controlled breeding and performance studies or by classical systematic analysis of phenotypic traits. Ecological, appending, parasite distribution, physiological and behavioural traits, morphometric and meristic.

It is depand on What is the objective that you need reach, because the level of DNA is beyond than what the morphology technic. The think is we cannot prove same by morphology. Understanding this only method that may help.

I made a thorough morphological study of Rafflesia and concluded that it is not an angiosperm. My paper 'Is Rafflesia an angiosperm?' was rejected by the journal I sent it to, on the grounds that molecular taxonomists have placed Rafflesia within or close to Euphorbiaceae and my question is irrelevant. I was shocked because in science there are no theories that are too sacred to be questioned. Also, one of the major functions of taxonomy is to explain the world of visible, tangible life forms i.e. the world of morphology. If an expert tells us not to believe our eyes and leave it to them to tell us what believe, then we are back in the age of sorcery. I got my paper published in JTFS with all the morphological evidence clearly displayed. This paper is fully illustrated with colour photos that one can zoom into to see a stunning new world.The paper can be downloaded freely from

https//doi.org/10.26525/jtfs2019.31.3.286

#Francis it was intersting, i am from Borneo, where rafflesia is also growth. You did the great method, but the analysis of the molecular is need have big picture. Usually for plant genome work is very expensive and very complex. I did many time and never finish. Usually we can look in transcriptomic level.

Francis S.P. Ng I'd love to have a copy of your paper on Rafflesia. JSTOR (your link below), does not allow free download and only excerpt and Abstract are available.

Thanks

• August 2019
• Journal of Tropical Forest Science 31(3):286-297
• DOI:

I don't work with taxonomy directly, but I believe this discussion needs to take into account mainly the behavioral and biogeographic aspects of the species we work with. In this way, I believe that the taxonomist should question how far morphological or genetic differences limit the coexistence of organisms and consequently their viable reproduction. I say this because in many cases research is restricted to the laboratory and aspects in situ are completely forgotten by many researchers. Morphological patterns may turn out to be simply phenotypic variations or polymorphism. In this sense, molecular studies (I am not an expert) may reveal genetic variations that may indirectly evidence long periods of reproductive isolation. Thus, according to molecular studies, species that were once treated as different today are the same, and species that were once treated as one are now revealed to be several species. You can find several examples in the literature in this regard. So, I think it is fundamental that a taxonomy work gathers molecular, morphological and mainly observations about its ecological aspects (habitat description, behavior, biogeographic context, population count, etc). Species are not magically created under a microscope or bar code. Taxonomists generally need to show in their descriptions how important environmental factors were to drive the evolution of that organism in its natural habitat. I have lost count of how many descriptions I have read and have only found the geographical coordinates of the specimen locations. Only that. As much as many treat this as mere speculation, I think we will cease to play our role as scientists if we do not question these ancient paradigms.

Molecular data are almost irreplaceable for reconstruction of phylogenetic relationships between genera or higher rank taxonomical units. However when it comes to species (what is a species?), same general problems are materializing as for alpha taxonomy: where is the boundary between species and infraspecific variations? However, if I had a chance to combine both molecular & morphological data for all of my taxonomical studies, I (and the scientific community) would only benefit from it.

I think Dr. Telnov has put his finger on the issue. No one thinks that Taxonomy will go away completely, and I would be happy if no one wrote any more impassioned defenses of basic taxonomy. The issue has always been that universities seem less willing to hire individuals who are simply taxonomists with no experience in phylogenetic systematics. If this is your issue you should probably try to find colleagues who do molecular work and collaborate.

Obviously you can identify a species by means of a molecular signature. Vice versa, however, it is not feasible to define species delimitations by DNA sequence features/differences. Here you face the same problems as with morphological characters: how large must these differences be to speak of different species. If there are clear and constant differences between sympatric 'populations' and you have unambiguously no hybridization, the case is clear! In my opinion, molecular and morphological data should be treated equally also from a phylogenetic view. Their classification as apo- or synapomorphies can be even-handedly done!

Nobody used the word "useless". If you want to be a university scientist you probably should become familiar with molecular techniques and findings. Please read the statements others make more carefully. The basic complaint made by several scholars is that pure Linnean style taxonomy has been supplanted by molecular approaches. This is a fact of 21st Century science. Morphological (and behavioral) data are still useful, but can be confusing because of convergence.

Dear Raymond,

beyond doubt you are aware that changes of DNA bases at distinct positions in different taxa can also be a case of convergence and are not necessarily synapomorphies. Furthermore a second base exchange at the same position can eventually reverse the effect which then becomes invisable. At the amino acid level such effects are more complex as changes can be due to alterations at different base positions of a triplet. The more complex the character the more reliable you can exclude such phenomenons. Thus, complex morphologial changes are reliable parameters as they usually will not - if at all - be reverted in the course of evolution.

I only intended to complement your notes!

Best wishes, Peter

Sorry to pose a so basic questions:

do you intend morphology-based (alpha) taxonomy devoted to find gaps among species (taxonomical units)?

My question is because a species is a biological concept grossly based on the ability of a certain group of individuals to reproduce themselves.

Allow me to present an example of the points I am trying to make. This is a recent work on the group (gulls of the genus Larus) on which I have done much of my research, including some basic taxonomy Article Recurrent hybridization and recent origin obscure phylogenet...

several taxonomists have looked at this group, however none of them anticipated the complexity suggested by this genetic analysis. I don't quite believe all of the links they reveal, but this shows that extensive hybridization and gene flow, which classical taxonomy cannot reveal, makes this group more of an international species flock than a subject that can be arranged according to basic taxonomy. Similar findings are appearing in a number of groups, including Cichlid fishes.

Basically these studies show that when hybridization takes place among non-sister taxa that things get very complex very rapidly. The basic assumption of most Taxonomists is that hybridization takes place primarily, if not exclusively between sister taxa, i.e. recently derived descendants of the same ancestor. Once this is no longer the case, taxonomists who do not use molecular approaches will never be able to resolve the relationships among groups of organisms that have undergone such introgression.

In relation to the question posed by Porcelli, of "a biological concept grossly based on the ability of a certain group of individuals to reproduce themselves" . may not really have much meaning and that if we wish to truly comprehend evolution that the Taxonomy argued for by many of the contributors to this debate, can make at best a limited contribution.

I regret this, because I am getting on in years and I thought that I understood evolution in Gulls, but these recent works suggest a much more complex and richer world, that classical taxonomy cannot adequately address.

Dear Francesco

I absolutely agree with you. But to test biological concept is almost imposible, thats why someone thinks that DNA is a solution, however I am not sure :-( But it helps a lot, if it's in right hands :-)

Dear Raymond

Yes, Hybridization is one of the biggest challenge for taxonomists and in that case DNA is really good tool for additional help, however still we are lacking some knowledge to judge and deside what will be enough to name species.

Thats why it needs "right hand".

I appreciate the positive feedback, and I agree, as I have said repeatedly, that Taxonomy has a place at the table. One of the points I made in my last response was that, although we can name species, DNA work is revealing that species may not be what we think they are, especially in groups where there is extensive gene flow between non-sister taxa like gulls and cichlid fishes. We may have to rethink our concepts, especially when it comes to what a Genus is. Keep in mind that a species name includes the genus.

Of course, YES,

the morphological method is the basis to identify the species,and molecular approach is the auxillary one to assist the morphological process,which can be great partner to figure out what it is, when and where it from.Seeing that the relationship between GENE and MORPHOLOGY, there will be intense combination in the near future to discover the unknown biosphere.

What's more, the genetic method can distinguish the cryptic species, which is of a vital role in the genetic diversity.

With so many species still to describe before extinction, I found this question is useless. It is not one or the other. We need all help available.

Once again, people are straying from the original question. The issue is about macrofauna and macroflora where there exists the opportunity to describe them based upon anatomy. Where single celled organisms are involved DNA is really the only way to assess diversity. Who cares if we describe species before they become extinct? The issue is to recognize and protect. as much diversity as possible

I don't think it is either morphology or DNA. Both can be used in species delimitation and description. If you follow the General Lineage Concept by DeQueiroz (i.e. species as independently evolving metapopulation lineages), you can apply different criteria to judge whether your are dealing with different species. Ideally, you take into account several criteria, such as morphology, genetics, behavior, etc. I have recently written a book chapter on this (focused on birds, but perhaps also relevant here): Chapter Avian Species Concepts in the Light of Genomics

In addition, there is the issue of cryptic species. Genetically divergent lineages that are morphologically almost identical. Here, DNA is needed to identify species. See for example this paper: Article Cryptic species as a window on diversity and conservation

Dear George,

Obviously, morphological taxonomy plays an important role, but that does not mean that it becomes superior to another method of analysis. Even if the morphological description provides all the necessary data to define a species, it does not mean that the analysis cannot be improved (molecular phylogeny or cases of Incertae sedis, for example). I agree that the morphological description can exist without the DNA analysis and that the opposite is not true, however, I also consider that both analyzes can work together in order to provide a even better result.

I am pleased that people keep restating the obvious, i.e. that combining DNA (genomics) , morphology, and behavior are all useful. This discussion started out with people claiming that classical taxonomy was not being taken seriously, and I tried to explain why this seemed to be the case, i.e. that Systematics, which incorporates DNA and genomics was supplanting Taxonomy based on morphology alone. Issues arise when DNA and morphology, behavior, and ecology do not line up well. As an example, in pinnipeds people have conceded to DNA when morphology, behavior, ecology and biogeography all suggest an alternative interpretation.

Also Dr. Ottenburghs states that "The origin of species is a gradual process that typically requires thousands to millions of years, creating a grey zone of species delimitation in which taxonomy is often controversial." How does this idea work with recent findings of species arising through introgression and hybridization that take only decades to forM?

In morphological classification, taxonomists identify species based on morphological characters. Scientists use DNA sequencing to confirm a new species. The essence of DNA sequencing is that, by comparing with a reference library of DNA sequences, an individual sequence can be used to identify an organism up to species level. Therefore, DNA sequencing helps taxonomists to confirm the new species after its morphological identification.

I think DNA sequencing technology is useful especially monitoring programs. There is limited of expertize all over the world. If biomonitoring programs all rely on morphological identification, there will be much possibility of error. The advantage of DNA sequencing is its robustness.

In my field, Entomology, Reviewers of various taxonomical papers of mine increasingly requested at least barcoding as a new tool of taxonomy to clarify the status and position of newly described species. Although it is not a requirement according to ICZN I can see in the future taxonomy will become DNA biased even in lower ranking journals. For journals of high recognition, application of various molecular methods was already a requirement (e.g. Systematic Entomology).

I do feel that morphological characters are still the best.Genitalic structures are good tools for reproductive isolation.In case of sibling species,species complexes,biotypesetc.Molecule characters r good.It is not possible to describe 1.75 million species on basis of molecular features.

Morphological characters are still the best most of our time

I perhaps may invite you to a related discussion: https://www.researchgate.net/post/Is_turbo-taxonomy_the_solution

All the best, Olli

As a taxonomist, I don't trust much of molecular analyzes for the following reason: the dubious description of new species based on the variation of sequences (DNA barcoding) in species of insects collected in hybridization zones is frequent in many scientific articles. The invention of new species through the technique of DNA barcoding is generating unprecedented confusion and taxonomical chaos in the delimitation of a species. The study of genetic crosses of populations in the field is more reliable to understand how genetic introgression works and not by means of a PCR that does not resolve differences in complex populations of a species. In molecular biology there are false positives that give rise to imaginary "species". It does not seem ethical to me to carry out meaningless studies with the aim of obtaining resources and funds.

Without detracting from the other fields of investigation, I think that the most valid systematic approach is the classical one on a morphological basis, as the morphological investigation allows us to differentiate in nature individuals who, due to their phenotypic characteristics, could be referred to either to the other entity (species, subspecies, variety) or to individuals or populations (swarms) of hybrid origin. Obviously, the valid application of this method strictly depends on the scholar's ability to identify constant qualitative characters and, as far as possible, to integrate the data acquired with those from other disciplines.

I totally agree morphological data is best for taxonomic studies, I think Molecular data only creating confusion, and yes for that first there is a need to do DNA sequencing of all available living entities.

I seriously think we are past the point of diminishing returns, because all defenders of Taxonomy say the same thing in slightly different words. Here is challenge for all of you. Describe the Taxonomic diversity of microorganisms with using DNA. There are no "imaginary species", and gene flow is just as big an issue for classical Taxonomy as it is for people who use DNA. If species have any validity it is as units of evolution and classical taxonomy is static in its descriptions, and as a result, it has difficulty evaluating rates of evolutionary change. The confusion exists because some people insist on acting as if species are fixed in time and space, which has never been true.

I think if morphological features are properly and critically defined, its foremost criteria of classification, DNA information comes later after the scrutiny of morphological taxo.

AKSrivastava

There are many examples where molecular techniques detected socalled cryptic species. When a skillful taxonomist examines the morphology he/she might find minute little details for morphological discrimination between these populations which perhaps would have been overlooked without the genetical hint.

I am still waiting for a classical taxonomist to discuss how they would classify single celled organisms without molecular data. It is fine to pontificate about birds and mammals, even insects and plants. Most species are single-celled and reproduce asexually. Any takers?

Each single taxon must be studied morphologically in order to recognize the most distinguishing characters, together with the species delimitation among its close relatives.

However, only DNA can prove the real position of each taxon due to different reasons such as homoplasy, phenotypic placticity, etc.

My final answer is YES, morphology is not always sufficient to define species, and we need DNA to help taxonomy.

Morphological attributes are still the best in majority of species.But DNA is an additional tool in cases of sibling/cryptic species. It is an excellent tool in cases of confusion,species complexes,biotypes but not every where and in each pecied.

The morphological identification of a species can be validated by molecular analysis to give an accurate account of the particular plant species.

Still no takers.. Come on I was hoping for more.

Morphological characters are still the best in most of our animal species.Genitalic attributes are so good in most of insect species.We must study additional taxonomic attributes of every species.Taxonomy has experienced a long journey from classical to molecular..We must pay respect to additional information coming to our way through modern attributes like accouslitcs,ethology, eco- taxonomy,llarval and cytotaxonomy