Cladistics - Science topic

Correct. All birds are dinosaurs (specifically, avian dinosaurs), but not all dinosaurs are birds. Pterodactyls are not dinosaurs; they are flying reptiles from the same era.

Yes, good point Phil Geis . We still have very little clue as to how life kicked off. A fascinating subject I love talking and thinking about, far more interesting than semantics of predator or parasite terminology.

We are not clad fish but clad apes. Though the Deep Ones are known among the lost tribes, who are worshipping the elder gods. For further reference, read up on the works of Abdul Alhazred.

What counts as a bird? If feathers are a sine qua non, then it's not inconceivable that some early featherless flying critters evolved into feathered flying critters, in which case their birdhood evolved after the capacity for flight. Note that I said "some". The evolution of birds might have taken several paths with different sequences from a common nonbird ancestor.

Of the living birds, the birds of the infraclass Palaeognathae are the closest to alligators: Ostriches, Rheas, Tinamous etc....

You're welcome Omkar Damle

MEGA 6, Saludos

Hey Satish Maurya !

you can just copy paste the selected range using ctrl+v and ctrl+v as long as the selected range is selected on the mesquite matrix. So for example, if you want to copy a range of 3 rows and 3 columns from the excel, you have to copy that range and go to the mesquite matrix and select 3 rows and 3 columns then paste it.

You might try PAUP 4 as it is designed for parsimony analysis too and does the bootstrap as well as a few other parsimony measures. Perhaps if you ran it on a public server you could let it run longer. I like the Cipres Portal (https://www.phylo.org/restusers/login.action).

On the other hand, I suspect that you will still get very small bootstrap values and perhaps even smaller if you use the more complex model. This is because the bootstrap samples your data with replacement (so it is the same size as the original sample). Naturally some informative data will not be sampled at all for a given replicate and others may be sampled more than once. The idea is that a data set with strong phylogenetic signal will be included in many replicates while a small amount of signal which may have influenced the original tree will not be sampled in as many replicates. The bootstrap proportion is the number of times a particular pattern in your data is sampled divided by the total number number of replicates. So seldom sampled rare phylogenetic patterns will appear in only a small proportion of the replicates. With 500 replicates a value of 10 means that only 50 trees (10%) will have that branching pattern (clade). If the data is rich in phylogenetically informative data that has consistent patterns rather than conflicting patterns then you will get high bootstrap values.

Unfortunately the bootstrap does not recognized whether you model is good or not except in the sense that a complex model requires more parameters and so will require many more unique patterns to resolve the tree. As an aside, this is exactly why genomic-sized phylogenies almost always have very high bootstrap values. But as they are very large data sets, computers cannot yet compute trees with any but the most simple models with a few parameters. These models often do not adequately model the complexity of sequence evolutionary history and so the simple models are biased and provide very high support for the wrong tree. The same holds for any kind of statistical analysis. A poor model will give biased results. So your simple model may not be at all a good idea. On the other hand your data may be too limited to fully resolve the tree.

However, all is not lost, because we are often not interested in having high support for every single branch or clade. Perhaps you only want to know a-priori whether a certain clade is monophyletic. And suppose your data has enough data to resolve that particular clade. Then the support on the other clades is much less important than finding good support for your clade of interest.

Also you can in some programs (TNT I think, and PAUP I know) perform a Templeton (a paired test on the data for several trees - Kishino-Hsagawa for nucleotide data) test on your data by comparing the tree with monophyletic clade with trees that are not monophyletic. If the tree score is the same for both tree topologies then you can at least say that you monophyly cannot be rejected. Or if one tree is significantly better than another then you can say with confidence that you reject the other tree.

Should you need more advice please contact me again. This is a very common problem for phylogenetics in general.

Some of the comments seem to be based on misinterpretation of the terms "species" and "subspecies". Species is defined by evolutionary separation ("evolving separately from others and with its own unitary evolutionary role and tendencies"), i.e. by permanently broken gene flow (no, or at most only occasional and/or ineffective hybridization); if such [group of] population[-s] does not show clear morphological differences it is called "cryptic", but anyway it is a perfectly "good" species: morphological distinctiveness is irrelevant for the general definition of species category (but of course it may be useful as a "marker" in recognition of species in particular cases, e.g. in case of allochronic or allopatric populations - see the final paragraphs of the attached paper). On the other hand, subspecies is a "morpho-geographical" category: a not isolated reproductively but morphologically significantly (a "rule of thumb" criterion is Amadon's 75% rule) distinctive allo- or para-patric [group of] population[-s]; thus, "cryptic" species, as being morphologically indistinctive, can only in exceptional, never or but extremely rarely realized in practice, situations show subspecific differentition. Generally, the category of subspecies is very useful as largely generalized but highly informative illustration of patterns of geographic variability, in clarification of many ecological, evolutionary and/or palaeogeographic questions &c., but of course only if it is correctly interpreted and consistently applied!

Got it. Thank you!

From the small amount of information that you have provided, I think that you are operating at a fairly high level of pattern recognition. However, since you are dealing in part with phylogenies, you should be aware that some hominin cladograms are based on single specimens. For example, in the case of the meme "Homo floresiensis" the phylogenies are based on a single skull (LB1) that is developmentally abnormal, so the phylogenies are misleading.

Hi Phillip,

First, a 19 taxa data set is really small, and you don't need to use TNT New tech searches, that are strategies originally developed for extremelly large datasets, but with the final purpose of finding some shortest trees, but not all the shortest trees. You can simply do a implicit enumeration (that will find all the shortest trees), or several replications (e.g. 100) using the 'traditional searches'.

Second, the 'additional' politomies are not "created" by TNT. The program handles the trees uncollapsed during the searches (keeping the trees as fully dicotomic, even if some branches don't have characters supporting them). All the branches are collapsed in the tree when doing a consensus. Then, is most likely that the branches you lose (where the politomies are shown) are not supported for any character in your two trees.

You can collapse the branches after the search in New tech. menu, or in any of the searches menues (default option of the program is no collapse after searches).

Hope this helps.

Camilo

Check the attached articles.

This question certainly requires specification. The answers depend heavily on what you are actually want to now.

(1) Morphological evidence considered in total evidence studies; A wide range and the selection depends mostly on the morphological disparity of the lineage inferred. Thus, the answer depends on the lineage of taxa inferred.

(2) Morphological evidence considered in the discussion of studies employing molecular phylogenetic: Again, the answer depends on the organisms studied.

(3) Material used to extract DNA for molecular phylogenetic studies: Again, the answer depends on the organisms studied and the question asked.

The hypothetical answers has one thing in common: it depends very much on the organisms studied.

Dear Peter,

Thanks for your help, now I got it. I just wanted to test this analysis.

Best wishes.

Occurrence of a complex of plant species in any geographic location is an indication of the adaptability of the species in that complex to the prevalent conditions in the location being studied. Adaptability, in turn, is an expression of genes for survival and reproduction  in the location. Initial lot of plants in this population might have come from diverse locations by way of dispersal or migration through various means available. Together, migration and survival make-up the adaptive radiation. At this stage, the change in genes in any species in the complex may not be much different from those prevailing in the parent populations from which they are derived. With advancing time and concurrent changes in climate, the genes for adaptation may change by way of recombining with related species in the vicinity, by mutation or by both. This results in a significant change in the expression of these genes in the next generation that may lead one to consider that new species are emerging. Sometimes, related species may interbreed and the resulting hybrids may tetraploidize as happened in the evolution of several crop species like coffee, wheat etc. In these cases speciation events are more clearly discernible.

It is a very interesting – and still underexplored – research topic. Generally, the Soviet taxonomists were rather hostile towards cladism (= phylogenetic systematics). Hennig’s classical book on foundations of cladistics is still not translated into Russian, and the first benevolent surveys of this taxonomic phylosophy did not appear in the USSR until the late 1980s. Of course, now the situation is quite another. Cladistic methodology is accepted by anybody who wants to use it, and it is almost impossible to find a theoretical paper written in Russian to reject cladism as a ‘wrong’ methodology. However, most taxonomists of old generations are still working within pre-Hennigian paradygm. But I would like to place your question in a wider context. Generally speaking, any attitude towards cladism concerned with a problem: “should phylogeny be taken as a foundation of the system?” I have to note that there was a long tradition of decoupling taxonomy and phylogeny on theoretical basis in the Russian taxonomy. As long ago as in the 1920s, some prominent systematists of Russia insisted that the phylogeny cannot serve as the basis of a system. I mean chiefly zoologists since I am not very familiar with the works of Russian botanists on this subject. Some of these Russian authors who rejected phylogeny published not only in Russian. I’d recommend you to read two papers of Eugene Smirnov, a very interesting Russian theorist of taxonomy:Smirnoff E.S. 1924. Probleme der exakten Systematik und Wege zu ihrer Lösung. Zoologischer Anzeiger, 61: 1-14.

Smirnov E.S. 1925. The theory of type and the natural system. Ztschr. indukt. Abstannmungs- und Vererbungsiehre, 37: 28-66.

These texts contains explanation why the ‘phylogenetic taxonomy’ is wrong (according to Smirnov).

Another prominent Russian author of that time, Vladimir Beklemishev, also insisted that systematics must not use phylogenetic data at all. Unfortunately, his theoretical views were not published in language other than Russian.

Concerning the post-Hennigian time, the most articulated theoretical work aimed to bring arguments against cladism is:

Skarlato O.S., Starobogatov Ya.I. 1974. Phylogenetics and the building of a natural system. Trudy Zoologicheskogo Instituta AN SSSR, 43: 30-46. (in Russian only).

Discussing Hennig (1950), the authors conclude that his attempt to reform taxonomy “leads to a complete elimination of taxonomy as a scientific discipline” (Skarlato & Starobogatov, 1974: 32). I may add that Starobogatov was among the most influential theorist of taxonomy in USSR, and his methodological views have been read widely.

Well, it is a top of iceberg, of course. If you like to get more information about the Russian theoretical taxonomy (very peculiar and very interesting if to view it in comparison with the Western European thinking), please ask me more. I am sure that the hostility towards cladism in the Soviet taxonomic community has deep philosophical roots and cannot be viewed as a over-simmplified picture of ideological confrontational between ‘East’ and ‘West’.

I just found a study of leporid lagomorphs that tackles a similar problem and uses 3D landmarks for morphometrics and phylo-morphospace plots:

Kraatz B, Sherratt E. 2016. Evolutionary morphology of the rabbit skull. PeerJ 4:e2453 https://doi.org/10.7717/peerj.2453

A lectotype is necessarily designated from a series of syntypes. The type locality of the species is the conjunct of localities of all syntypes. By the designation of a lectotype, the type locality of the species becomes that of this specimen. In the case of syntypes without locality, the lectotype would not have a locality and, consequently, the species has not a type locality. It is not possible to designate a type locality posteriorly. An subsequent author can determine the distribution area for the species, but not a particular locality as the type locality of that species.

None of these methods are absolutely better than the others, philosophically, but different researchers, different fields, and more importantly different journals/reviewers will have their idiosyncrasies. If you're working in paleontology or with datasets that are missing a lot of data points, as is the case with a lot of paleontological phylogenetics, bootstrap/jackknife values are not expected to be as high as those with more complete (i.e. genetic) datasets. A bootstrap of <50% universally means that the clade is not well-supported, but depending on the field and the size of the dataset what constitutes a well-supported clade can change. >95% is always strong support, but depending on how rigorous you want to be/how much you hate polytomies it can be advisable to retain all clades with >50% support.

I respectfully submit that Frank has missed the point of the original question. Phenetics was a methodology, not a description of characters. It was the grouping and classification of organisms based on overall similarity, as opposed to Hennig's phylogenetic systematics (which became known as cladistics) which used special similarity (synapomorphy) to group and classify organisms. Those were the competing paradigms and while Hennig's basic ideas certainly won out over phenetics (see D. Hull's great book Science as a Process), phenetics is back on the rise. With the accumulation of massive genomic data sets, some folks are turning to phenetics as a way to analyze these data sets. 

I think the answer about clear phylogenetic lineages in humans is that, by the criteria used in drawing such lineages within other species, NO, Tha answer is fairly simple, but details are given in the two articles by my colleague Alan Templeton, cited above. The basic issue is this: For a species to be clearly subdivided into sub-groups (sub-species, or the older term "race"), using molecular (mitochrondrial DNA) evidence, the lineages must be clearly distinguishable (not overlapping) and the territories occupied fairly distinct, with little or no gene-flow between them. For our nearest evolutionary relatives, the chimps, (genus Pan troglodytes, there are five clear sub-species, each with several clear lineages within each sub-species. Using the same molecular approach, humans show no clea lineages at all within the Homo sapies. Our groups form one big blur on a mt-DNA tree. The reason is that for the entire period of our evolution from Homo erectus, hominid populations migrated and interbred to a degree not matched by any other animal species. While different human geograpphic populations do have differences in their genetic make-up, these differences are minor when compared to true sub-species in other animals. It was pointed out long ago (Richard Lewontin among many others) that there is more genetic variation within any given geographic population than between any two populations.I hope this helps.

I strongly disagree with their convention to list all taxa alphabetically. In almost every case there is a wealth of phylogenetic data showing that the taxa listed in adjacent positions in their linear classification are actually not closely related.

An example from birds: Psittaciformes (parrots and allies) is now known to be the sister taxon of Passeriformes (the songbirds), but these are not listed next to each other in this classification. Any classification that does not reflect such knowledge, is not going to be taken seriously by specialists and is doing a disservice to its (non-specialist) end-users.

And even if taxa are correctly placed next to each other in a list of multiple taxa, they could not be placed in a separate taxon because the relevant rank was not used by the authors. For instance, Archosauria (the clade containing crocodiles and birds) could not be recognized. Thus, the new classification disregards a huge body of knowledge because the authors limited their endeavor to a small number of ranks.

This is a classification of living organisms but it is unlear how extinct clades can be accomodated in this system. This is not a trivial issue given that >95% of taxa are extinct. For instance, Aves (birds) is listed as a subclass of Reptilia, but there is no indication how the large number of splits in the phylogeny between the origin of Reptilia and the origin of Aves are going to be ranked.

Another problem is how sister taxa are listed. If two taxa are sisters, current practice (albeit mostly implicit) is to list the smallest clade before the largest. In ornithology, ALL modern authors place Palaeognathae (ostriches, kiwis, etc) before Neognathae ('modern' birds) because the former is the smaller clade. In the classification by Ruggiero et al. (2015), the order is reversed because N comes before P in the alphabet. I doubt that anyone in ornithology is going to use this.

This could have been avoided (i) if the ambitions of the authors were a bit higher, (ii) if the level of detail (structure) of the classification was based on actual phylogenetic knowledge, rather than a small set of ranks, (iii) and if the authors had sought the help from specialists.

A rankless system (i) would have given the authors the freedom to recognize additional clades and resulted in a much better reflection of current phylogenetic knowledge, and (ii) avoided pointless 'debate' about the 'appropriate' rank of any given taxon.

However, even with a ranked system much more could have been done with all the phylogenetic knowledge that is already available.

You get that problem all the time with morphological data: Loose definitions of character states result in a wide range of morphologies considered as similar which would be regarded as incompatible if more strict criteria for similarity had been applied. As a consequence the measured amount of homoplasy (in a cladistic analysis) is higher in case of loose definitions and few incompatibilities than for strict definitions and many incompatibilites. But that appears to be rather trivial ...

I think the Taguchi-Maharanobis strategy is proper for your inquiry.

We consider each reference samples as each classes and one individual as the other class. This is the same as one-class SVM.

I developed the optimal LDF on the minimum number of misclassisications (MNM).

We discriminate the data consists of reference samples with one individual.

We evaluate the discriminant scores by obtained LDFs and choose reference calass with the most biggest t-value.

I am willing to co-work.

Ortholog - similar genes in different species.

Paralog - similar genes within a species.

Homologs - Orthologs and Paralogs.

Dear Daniel,

Why worms?

I can't recommend the Wilkinson et al. (2007) paper Enelise suggested. But if you are looking for a predator feeding on ostracods you may check the paper of Elawa 2007 "Predation on Miocene ostracods of Wadi Um Ashtan" in the same volume.

It would be helpful to get more information on your findings to give a reliable answer. The paper Axelle suggested mentioned one possibility, Malcom's answer too. Additionally, it could also be a coprolite of a larger organism (e.g. fish)* or a lining of a burrow instead a filling (Ophiomorpha-like). Another possibility is a variation of one of Jens' suggestions: the second use of a burrow enriched with organics by "farming" by ostracods.

You should add pictures, information of shape and suggestions about the former 3-dimensional structure of your findings, as well as information about the ostracods (single valves or carapaces?, species?, monospecific assemblage?, size distibution among the individuals?, ect.)

Best regards

Johannes

*Pollard 1985 Coprolites and ostracods from the Dinantian of Foulden, Berwickshire, Scotland. Earth and Environmental Science Transactions of the Royal Society of Edinburgh, 76(01):49 - 51

Koshla et al. 2015 Ostracods, plant tissues, and other inclusions in coprolites from the Late Cretaceous Lameta Formation at Pisdura, India: Taphonomical and palaeoecological implications. Palaeogeography Palaeoclimatology Palaeoecology, 418(418):90-100.

Yes, your question is a bit vague. The character coding decisions (including binary vs. multistate characters) depends on the type of characters you work with (e.g., molecular vs. morphological data) the purpose of the analysis (e.g., phylogenetic tree inference vs. reconstruction of character evolution) and the a priori knowledge about the character evolution and character state distribution across taxa of interest. You order a transformation series (i.e., a group of homologous characters) if you believe that there is a particular path of evolution for that group of characters. Additive vs. non-additive character states is an issue only when coding multistate characters. If you assume a particular ordering of character state change, you code the character as additive. (An example of additive multistate character is three-state character describing body size: 0 (small) <-> 1 (medium) <->  2 (large) where change from state 0 to 2 is more costly than change from 0 and 1 or vice versa. On the other hand, a similar character describing body coloration: 0 (red); 1 (green); 2 (blue) would be considered unordered with number of steps between each character state being equal). The multistate character ordering (as well as polarity and reversibility) can greatly influence the outcome of phylogenetic analysis and is worth experimenting with (that is, if you work with manageable amount of characters). I recommend you to begin with the following article:

The letters beginning with the ">" symbol are located at the internal nodes and stand for pruned taxa that, when included in the analysis, would be placed within a polytomy. One or more taxa can descend from a single node. The letters not beginning with a ">" symbol are located at the tips and stand for pruned taxa that, when included in the analysis, would be placed as a sister taxon of a single terminal.

I think very interesting placement of Crother. However, I worry how this is being done today. I think that current approaches are too simplistic. Do not take into account a number of empirical knowledge that we have about the distribution of species. Thus, what I mean is: It may even be possible to estimate an ancestral area, but it is not a simple task as rebuilding an ancestral state of a character in a phylogeny (at least in the most cases).

Hi Steven,

You can calculate Robinson-Foulds and SPR distance between trees on TNT. For Robinson-Foulds distance you need a script, available at http://tnt.insectmuseum.org/index.php/Scripts 

SPR distance calculation is on the menu Trees/Comparisons

Hope this helps,

Camilo

If the matrix (specifically number of taxa) is small enough, you could try implicit enumeration, the equivalent of branch and bound in PAUP*. Unlike traditional search, it will always find all shortest trees, guaranteed. The main problem is that it takes longer than the other types of parsimony searches, so it is only reasonable for small numbers of taxa.

If you just want to have a better CI and RI using the new technology search won't help you. with this amount of taxa and characters I do not think you will find a distinct topology, and the length will probably be the same, almost for sure.  For such a small analysis TNT works well with the traditional search. This can not be the case for you, but I would just say that the CI and RI you have may be related to the small number of characters compared to the number of taxa in your analysis. 

You have to check the "collapsing rules" that you are using. Collapsing rules are used for to collapse unsuported branches. By default, PAUP uses collapsing rule 3 (if some optimization implies support, keep branch ). TNT by default use rule 1 (collapse branch if some optimization lacks support). Rule 1 is much stronger than rule 3, and by consequence, consider less trees as different, giving you "less" trees than PAUP. If you choose rule 3 on TNT (Settings/Collapsing rules/ max length = 0), you will get the same trees than in PAUP. The difference in length is most probably due to different parameters of the analysys. Both programs, using the same paremeters, must give you trees of the same length.

In phylogeny most realistic tree = most stable tree topology built by different methods. If we use bootstrap, we can estimate how many times structure of some nodes are identical. As for many algorythms it's need to note that they based different computational models. Also if we will obtain same or similarstructure of phylogenetic tree by using different algorhythms (i.e. ML, MP, NJ or others), will mean that such topology can be realistic.

Dear George,

my view is this: there is no simple parallelism.

- Monophyly is recognized by shared synapomorphies;

- Paraphyly also needs synapomorphies to be recognized at all, but often involves homoplasies (in the form of reversals), and of course plesiomorphies;

- Polyphyly is likely when synapomorphies are absent and homoplasies dominate, but plesiomorphies are abundant as well.

- Monophyly is a hypothesis of relationship, synapomorphy is a character-state indicating potential relationship between taxa.

Cheers

Rainer

To Ahmed Alzohairy,

The question which should be asked here - what do words 'great similarity' mean?

If it just imply that there are great structural similarity and, for some extend, similarity of their sequences, than it is not surprising because viruses derived from retrotransposons and they share many common features. The essential enzymes have very conserved domains which possess great similarity to each other from different retrotransposon and viruses.

However, there is also another layer to this question. If we are talking about particular genome, e.g. human, we have to remember that some retrovirus sequences can be captured by genome and become internalized and vertically transmitted from progenitor to progeny; but it does not change the fact that originally viruses derived from retrotransposons through several steps of modular evolution.

The rules I follow are: 1) preserve traditional nomenclature for groups as long as they are monophyletic. 2) only name taxa that require new names (e. g. converting a traditional named "group" that is paraphyletic into two or more clades, one of which may need a name). 3) Use the widely-accepted code of nomenclature for your organisms (ICZN, ICN for botany) and not the "Phylocode" which does not have any formal standing in biological nomenclature and is not used by anyone other than its sparse but vociferous proponents.