While working for a 2-piece post service on the Genealogical World of Networks (A fleck of heresy: networks for matrices used inward Cladistics studies), I stepped over a threat on ResearchGate, where someone asked this. I browsed through the answers, in addition to felt obliged to respond equally well.
[The next is a fairly literal re-create of my respond on RG, graphics are added]
Cladistics is virtually clades, defined equally subtrees inward rooted trees. There's a prissy chapter inward Joe Felsenstein's 2004 book, Inferring Phylogenies, on this; also pointing out why nosotros genuinely should clearly distinguish betwixt clades, a subtree inward a rooted graph, in addition to monophyla, an interpretative concept. It goes dorsum to Farris (1983) in addition to non Hennig (1950).
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| An inferred tree: all but ane subtree tin live diagnosed past times cast features. Members of genus Oval are business office of the all-rounded subtree, but the olive Oval is sis to a subtree comprising Donut and the royal Oval. |
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| By rooting the tree using the outgroup, the subtrees travel clades in addition to nosotros tin position names to the clades. Either branch-based (bold internodes) or node-based (dots representing the hypothetical 'most-recent mutual ancestor' — MRCA). Only nether the supposition that the inferred tree reflects the truthful evolutionary tree, such a cladistic classification is a phylogenetic classification. |
Hennig "just" provided a novel (indeed better, because it tin live tested) concept for monophyly inward the framework of his "Kladistik" (which differs inward quite some bits from what afterwards became "Cladistics")
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| The work Hennig tried (half succeeded, one-half failed) to solve: development of 2 reciprocally ("mutually") monophyletic lineages, Roundish (all descendants of Rounded) and Pointish (all descendants of Pointed), inward fourth dimension in addition to morphospace. Note each cladogenesis, i.e. dichotomous split, is accompanied past times a unique alter inward cast or colour. But whereas forms exclusively evolved once, i.e. are or were(!) synapomorphies, colours were also evolved inward parallel (lush bluish octagon) or independently inward the Roundish and Pointish lineages (olives). | |||||||||
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| Realising that cast is to a greater extent than of import than colour, nosotros tin position upwards an intuitive phylogenetic classification: all groups travel dorsum to a defined mutual ancestor, i.e. are monophyletic (in a pre-Hennigian sense). Hennig noted the difference betwixt groups of inclusive mutual origin, his monophyla (green; Let's distinguish betwixt Hennig in addition to Cladistics PS Statements [see Victor Orrico's respond on RG] that NJ trees are "phenetic" are incorrect (a mutual error): the NJ algorithm produces phylogenetic trees fulfilling either the minimum development (ME) or least-squares (LS) optimality criteria (depending how laid up). The algorithms for UPGMA in addition to NJ are both cluster-algorithms (so "phenetic", if y'all want), but for the NJ it has been shown that it succeeds inward finding a expert gauge for the ME or LS tree (which UPGMA does exclusively past times accident). NJ is only a shortcut to notice a ME or LS-optimised phylogenetic tree from a distance matrix (again e.g. Felstenstein, 2004, Înferring Phylogenies). H5N1 perfect matrix, where each cladogenesis is represented past times at to the lowest degree 2 subsequent synapomorphies volition number inward a perfect distance matrix, in addition to the ME or LS tree inferred from this matrix, volition live the truthful tree, in addition to identical to the unmarried MPT inferred from the grapheme matrix. If convergences outcompete synapomorphies, the MPT volition take away keep clades that are non monophyletic, equally volition (to a lesser grade it seems) the ME or LS tree, whereas compatibility in addition to probabilistic methods tin grip this to some degree. Phylogenetics is virtually phylogeny, evolutionary pathways, in addition to goes dorsum to Darwin in addition to Wallace's age. The kickoff phylogenetic trees were published inward the 19th century, ane of the earliest at my Alma mater, the University of Tübingen, past times Franz-Martin Hilgendorf (who also published maybe the kickoff phylogenetic network). Haeckel did a lot to advocate phylogenetic trees, in addition to also coined monophyly, if I retrieve correctly). Regarding kickoff phylogenetic trees including a Definition of what a phylogenetic tree is, run across this post service past times David Morrison [Side-remark: H5N1 phylogenetic tree is a tree depicting ancestor-descendant relationships, which, ironically, no cladogram, the silent commonly seen rooted trees without branch lengths, can; in addition to phylograms, rooted trees amongst branch lengths, exclusively indirectly past times zero-length terminal branches.]
I gave it a quick search, in addition to works life this prissy laid of lecture slides giving a quite comprehensive introduction into "evolutionary (phylogenetic) trees" in addition to iii of the methods to infer them: "Parsimony; Distance matrix based; Maximum likelihood" [link to PDF]. Cladistics is thus a (quite restricted) subset of phylogenetics (not synonymous amongst Hennig's "Kladistik"). So, to live on the rubber side, ever travel for phylogenetics.
And largely irrelevant these days. Not a few are aware (openly or shyly) that clades inward rooted trees often correspond to monophyla, i.e. groups of inclusive mutual origin, but non necessarily reach so. Incomplete lineage sorting is cladistics' greatest foe. Just convey the many cases where dissimilar genomes tell dissimilar stories: the nuclear, mitochondrial and/or plastid trees may take away keep dissimilar highly supported clades, but at that topographic point tin exclusively live ane monophylum (or 2 overlapping ones, inward instance of hybridisation). Which nosotros elbow grease to infer based e.g. on the coalescent tree (which is a special cast of coalescent network). Or, mean value of a misplaced root or ingroup-outgroup long-branch attraction that easily plough a grade into a clade an vice versa. Especially parsimony trees tin live severely misleading (see eg. this recent newspaper past times Scotland RW, Steel M. 2015. Circumstances inward which parsimony but non compatibility volition live provably misleading. Systematic Biology 64:492–504).
Plus, at that topographic point are many evolutionary/biological processes that inflict reticulation, i.e. ancestor-descendant relationships that cannot live modelled past times a tree at all. H5N1 phylogenetic tree is only a special phylogenetic network, i.e. a phylogenetic network without reticulation. H5N1 notable exception is classification. Cladistic classification, putting names to clades inward inferred trees (under the implicit supposition that all clades stand upwards for monophyla fide Hennig), is silent the holy goal. Although, nosotros often curvature the rules in addition to role (more general) phylogenetic classification concepts. Oaks beingness an example: the kickoff multigene trees placed them inward 2 separated, well-supported clades, but no-one was bold plenty to split upwards this (most probable monophyletic) genus into 2 genera plumbing equipment the 2 clades inward the trees or include the chestnuts etc. inward the oaks. We formalised the 2 oak clades lastly twelvemonth equally subgenera (paywalled final version; free Pre-Print amongst ane major change: Ponticae and Virentes accepted equally additional sections inward lastly version), the novel infrageneric classification of oaks is thus a cladistic ane based on nuclear oligo-gene in addition to phylogenomic trees. But nosotros are confident that it is also a phylogenetic one: our subgenera in addition to sections are non exclusively clades, but also monophyla (today in addition to dorsum into the past). Cladistic or Hennig-phylogenetic classification (e.g. PhyloCode, using 'clade' equally synonym for 'monophylum') is, however, impractical (to impossible, run across e.g. Brummit 2002, How to chop upwards a tree) when beingness extended to fossils, nosotros summarised the dissimilar concepts (those used inward reality) inward Fig. 8 of our 2017 Osmundales paper (open access). Naming (likely) paraphyla, or groups that may live para- or monophyletic, is inevitable. Ancestral forms in addition to groups demand names, besides (no cite of fossil/ancestral taxa inward the PhyloCode). Why is at that topographic point so much confusion? Apparently many silent hang on to parts of the 80s intellectual cladist bundle equally summarised past times Joe Felsenstein this listing tin live works life inward his 2001 slice for Systematic Biology, opened upwards access). So y'all non rarely instruct strange (and wrong) comments from (anonymous) reviewers (I got them quite often, since I normally used networks for phylogenetics in addition to often had to bargain amongst fundamentally "a-cladistic" data) Quoted from Felsenstein (Syst. Biol., 2001, p. 466): "The cladists of that era had accepted a number of points equally an intellectual package. At ane betoken inward the mid-1980s I tried to summarize the bundle in addition to came upwards amongst these points, inward lodge of importance
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