Ockham's Razor applied, but not used: can we do DNA-scaffolding with seven characters?

One of the most interesting research areas in organismal science is the cross-road between palaeontology and neontology, which puts together a picture marrying the fossil record with molecular-based phylogenies. Unfortunately, when it comes to plant (palaeo-)phylogenetics, some people adhere to outdated analysis frameworks (sometimes with little data).

How to place a fossil?

The fossil record is crucial for neontology as it can provide age constraints (minimum ages when doing node dating) and inform us about the past distribution of a lineage. This, especially in the case of plants that can't run away from unfortunate habitat changes, can be much different than today.

The main question in this context is whether a fossil represents the stem, ie. a precursor or extinct ancient sister lineage, or the crown group, ie. a modern-day taxon (primarily modern-day genus). For instance, the oldest crown fossil gives the best-possible minimum age for the stem (root) age of a modern lineage, whereas a stem fossil can give (at best) only a rough estimate for the crown age of the next-larger taxon/clade when doing the common node dating of molecular trees (note that fossilized birth-death dating can make use of both).

There are two commonly accepted criteria to identify a crown-group fossil:

1. Apomorphy-based argues that if a fossil shows a uniquely derived character (ie. a aut- or synapomorphy sensu Hennig) or character suite diagnostic for a modern-day genus, it represents a crown-group fossil.
2. Phylogeny-based aims to place the fossil in a phylogenetic framework, the position of the fossil in the genus- or species-level tree (most commonly done) or network (rarely done but producing much less biased or flawed results) then informs what it is.

(We will focus on members of modern-day genera, since it becomes more trickier for higher-level taxa, see eg. my posts thinking about What is an angiosperm? [part1][part2][why I pondered about it].)

There a three basic options to place a fossil using a phylogenetic tree.

1. Putting up a morphological matrix, then inferring the tree. A classic but due to the nature of most morphological data sets leading to a partly wrong tree as we demonstrated in some posts here on the Genealogical World of Phylogenetic Networks (hence, such analysis should always be done in a network-based exploratory data analysis framework).
2. Putting up a mixed molecular-morphological matrix, then inferring a "total evidence" tree. This includes sophisticated approaches that use the molecular data to implement weights on the morphological traits and/or consider the age of the fossils (so-called total evidence dating approaches). Works not that bad with animal-data, provided the matrix includes a lot of morphological traits reflecting aspects of the (molecular-based) phylogeny. Doesn't work too well for plants because we usually have much fewer scorable traits, most of which are evolved convergently or in parallel. Non-trivial plant fossils love to act as rogues during phylogenetic inference.
3. Optimise the position of a fossil in a molecular-based tree, eg. using so-called "DNA scaffold approach" (usually using parsimony as optimality criterion) or the evolutionary placement algorithm implemented in RAxML (using maximum likelihood). A special form of this approach is to first map the traits on a (dated) molecular tree, and then find the position where a fossil would fit best.

Why (standard) phylogenetic tree-based approaches are tricky

Below a simple example, including three fossils of different age (and often, place) with different character suites.

Even though none of the derived traits (blue and red "1") is a synapomorphy (fide Hennig), we can assign the youngest fossil X to the lineage of genus 1A just based just based on its unique derived ('apomorphic') character suite. Its likely a crown-group fossil of clade 1, and may inform a minimum age for the most-recent common ancestor (MRCA) of the two modern-day genera of Clade 1.
Apomorphy-wise, fossils Y and Z cannot be unambiguously placed. The red trait appears to be independently obtained in both clades, and the blue trait may have been

• a synapomorphy of the whole ingroup (Clade 1+2) till some point in time, lost in the genus 2B-2C lineage, ie. a symplesiomorphy sensu Hennig, or
• a parallelism / homoiology (see also Has homoiology been neglected in phylogenetics?)

To discern between the options, we'd be well-advised to do character mapping in a probabilistic framework which require a tree with independently defined branch-lengths.

Just by using parsimony-based DNA-scaffolding, fossil X would be confirmed as crown-group fossil and member of genus 1A (being identical and different from all others) and fossil Z would end up as a stem-group fossil. Fossil Y, however, would be placed as sister to genus 2C (again, identical to each other and different from all others). Using Y in node dating, would then lead to a much too old divergence age for the crown-group age of Clade 2. In reality, what researchers do with such a seemingly too old fossil is not to use it by the book, as MRCA of Genus 2B and 2C, but to inform the MRCA of eg. genera 2A, 2B, and 2C assuming that the fossil's age and trait set indicate the 2C morphology is primitive within the clade or Y is an extinct sister lineage and the shared derived trait a convergence (parallelism).

Four characters, three homoplastic and one invariant, are surely not enough for DNA-scaffolding, but adding more and more characters has a catch. Easy to do for the modern-day taxa, for which we also have molecular data, the preservation of fossils limits adding many more traits; any trait not preserved in the fossil is effectively useless when placing it (including not-preserved traits in total evidence approach may, nonetheless, help the analysis). Which brings us to the real-world example just published in Science:

Wilf P, Nixon KC, Gandolfo MA, Cúneo RA (2019). Eocene Fagaceae from Patagonia and Gondwanan legacy in Asian rainforests. Science 364, 972. Full-text article at Science website.

Why one should not place a fossil using DNA-scaffolding with seven characters

Wilf et al. show (another) spectacularly preserved fossil from the Eocene of Patagonia. Personally, I think that just publishing and shortly describing such a beautiful fossil should be enough to get into the leading biological journals.

But Wilf et al. wanted (needed?) more and came up with the following "phylogenetic analysis" to argue that their fossil is a crown-group Castanoideae, a representative of the modern-day firmly Southeast Asian tropical-subtropical genus Castanopsis, and evidence for a "southern route to Asia hypothesis" (via Antarctica and Australia, both well-studied but devoid so far of any Fagaceae presence; despite the fact that the modern-day climate allows cultivating them as eg. source for commercially used wood).

Wilf et al's Fig. 3 and Table 1 suggest to me that the paper was not critically reviewed by anyone familiar with the molecular genetics of Fagaceae or phylogenetic methods in general — perhaps this is not needed, since the first author is well-merited and the second author a world-leading expert of botanical palaeo-cladistics. However, parsimony-based DNA-scaffolding can be tricky, even with a larger set of characters (see eg. the post on Juglandaceae using a well-done matrix), and using seven is therefore quite bold. Notably, of the seven characters, one is parsimony-uninformative and four are variable within at least one of the included OTUs.

Side note: The tree used as a backbone is outdated and not comprehensive. Plastid and nuclear-molecular data indicate that the castanoids Lithocarpus (mostly tropical SE Asia) and Chrysolepis (temperate N. America) may be sisters. However, the morphologically quite similar Notholithocarpus is not related to either of these, but is instead a close relative of the ubiquitous oaks, genus Quercus (not included in Wilf et al.'s backbone tree), especially subgenus Quercus. Furthermore, the (today Eurasian) castanoid sisterpair Castanea (temperate)-Castanopsis (tropical-subtropical) have stronger affinities to the (today and in the past) Eurasian oaks of subgenus Cerris. The Fagaceae also include three distinct monotypic relict genera, the "trigonobalanoids" Formanodendron and Trigonobalanus, SE Asia, and Colombobalanus from Columbia, South America. Using a more up-to-date instead of a 2-decade-old molecular hypothesis would have been a fair request during review, as would compiling a new molecular matrix to infer a tree used as backbone (currently gene banks include > 238,000 nucleotide DNA accessions including complete plastomes). This would have also enabled the authors to map their traits using a probabilistic framework, which can protect to some degree against homoplastic bias but requires a backbone tree with defined branch-lengths.

There are many more problems with the paper and its conclusions, but this critique would be content- not network-related. Let's just look at the data and see why Wilf et al. would have better off not showing any phylogenetic analysis at all (and the impact-driven editors and positive-meaning reviewers should have advised against it). Or a network.

Clades with little character support

The scaffolding placed the Eocene fossil in a clade with both representatives of Castanopsis, from which it differs by 0–2 and 1–4 traits, respectively. Phylogeny-based, the fossil is a stem- or crown-Castanopsis.

However, the fossil has a character suite that differs in just a single trait (#6: valve deshiscence) from the (genetically very distant) sister taxon of all other Fagaceae, Fagus (the beech), used here as the outgroup to root the Castanoideae subtree. As far as apomorphies are concerned, the data are inconclusive as to whether the fossil represents a stem-Castanoideae (or extinct Fagaceae lineage) or a Castanopsis — this critical, potentially diagnostic derived trait, partial valve dehiscence, is only shared by the fossil and some but not all modern-day Castanopsis. This particular trait is not mentioned elsewhere in the text, although it is the reason the fossil is placed next to Castanopsis and not the outgroup Fagus in the "phylogenetic analysis".

In the following figure, I have mapped (with parsimony) the putative character mutations on the tree used by Wilf et al.

Black font: shared by Fagus (outgroup) and "Castanoideae". Green font: potential uniquely derived traits. Blue font: traits reconstructed as having evolved in parallel/convergently. Red branches, clades in the used backbone tree that are at odds with currently available molecular data (the N. American relict Notholithocarpus should be sister to the Eurasian Castanea-Castanopsis).

This hardly presents a strong case of crown-group assignation. Except for partial dehiscence, even the modern-day Castanopsis have little discriminating derived traits — they are living fossils with a primitive ('plesiomorphic') character suite. Intriguingly, they are also genetically less derived than other Castanoideae and the oaks (see eg. the ITS tree in Denk & Grimm 2010).

The actual differentiation pattern

The best way to depict what the character set provides as information for placing the fossil is, of course, the Neighbor-net, as shown next.

Neighbor-net based on Wilf et al.'s seven scored morphological traits used to place the fossil. Green: the current molecular-based phylogenetic synopsis — based mostly on Oh & Manos 2008; Manos et al. 2008; Denk & Grimm 2010. I had the opportunity to get familiar with all of the then-available genetic data when harvesting all Fagaceae data from gene banks in 2012 for a talk in Bordeaux. One complication in getting an all-Fagaceae-tree is that plastids, geographically constrained, and nuclear regions tell partly different stories.

Castanopsis, including the fossil, is morphologically a paraphyletic (see also our other posts dealing with paraphyla represented as clades in trees). Note also the long edge-bundle separating the temperate Chrysolepis and chestnuts (Castanea), from their respective cold-intolerant sister genera (Lithocarpus viz Castanopsis) — derived traits have been accumulated in parallel within the "Castanoideae". The scored aspects of Fagaceae morphology are very flexible and ~50 million years is a long time, possibly leading to partial valve indehiscence (or losing it) without being part of the same generic lineage. The puzzling differentiation, and the profoundly primitive appearance of the fossil (shared with modern-day Castanopsis), may in fact be the reason the authors didn't: (i) optimize / discuss very similar, co-eval fossils from the Northern Hemisphere interpreted (and cited) as extinct genera (eg. Crepet & Nixon 1989), (ii) left out the two Fagaceae genera today occurring in South America, (iii) opted for classic parsimony and a partly outdated molecular hypothesis, and (iv) just showed a naked cladogram without branch support values as the result of their "phylogenetic analysis" (Please stop using cladograms!)

Based on the scored characters, the position of the fossil in the graph, and on the background of a more up-to-date molecular-based phylogenetic synopsis (the green tree in the figure above), the most parsimonious interpretation (and probably, the most likely) is that the fossil may indeed be a stem-Castanoideae, a representative of the lineage from which the Laurasian oaks evolved at least 55 million yrs ago (oldest Quercus fossil was found in SE Asia), or even represent a morphologically primitive, extinct (South) American lineage of the Fagaceae. Regarding the "southern route", Ockham's Razor would favor that they are just a South American extension of the widespread Eocene Laurasian Fagaceae / Castanoideae, since very similar fossils and castaneoid pollen is found in equally old and older sites in North America, Greenland (papers cited by Wilf et al.) and Eurasia but not Australia, New Zealand or Antarctica.

A final note: when you have so few characters to compare, you should use OTUs that are not completely ambiguous in every potentially discriminating character, as scored for the "C. fissa group" — the "Castanopsis group" has a single unambiguously defined, potentially derived trait. Using artificial bulk taxa is generally a bad idea when mapping trait evolution onto a molecular backbone tree. Instead, you should compile a representative placeholder taxa set, with as many taxa as you need (or are feasible) to represent all character combinations seen in the modern species/genera.

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Postscriptum (14/1/2020)
Relevant matrices (NEXUS-formatted) and explicit character trait maps (Why we want to map trait evolution on networks, pt.1 – Introduction, pt.2 – Topological Ambiguity) have been uploaded to figshare.

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Other cited references, with comments

Crepet WL, Nixon KC (1989) Earliest megafossil evidence of Fagaceae: phylogenetic and biogeographic implications. American Journal of Botany 76: 842–855. – introducing a Castanopsis-like infructescence interpreted to represent an extinct genus but very similar to the new Patagonian fossil in its preserved features; and co-occuring with castaneoid pollen (not reported so far for Patagonia) and foliage.
 
Denk T, Grimm GW (2010) The oaks of western Eurasia: traditional classifications and evidence from two nuclear markers. Taxon 59: 351–366. — includes an all-"Quercaceae" ITS-tree (fig. 3) and -network (fig. 4) using data of ~ 1000 ITS accessions; the nuclear-encoded ITS is so far the only comprehensively sampled gene region that gets the genera and main intra-generic lineages apart (recently confirmed and refined by NGS phylogenomic data), something wide-sampled plastid barcodes struggle with. Analysed with up-to-date methods and avoiding long-branch interference by excluding the only partially alignable Fagus, Castanopsis dissolves into a grade in the all-accessions tree and Quercus is deeply nested within the Castanoideae (as already seen in the 2001 tree used by Wilf et al. as backbone). The species-level PBC neighbor-net prefers a ciruclar arrangement in which Notholithocarpus remains a putative sister of substantially divergent and diversified Quercus, followed by Castanea-Castanopsis, and Lithocarpus, while Chrysolepis is recognized as unique.

Oh S-H, Manos PS (2008) Molecular phylogenetics and cupule evolution in Fagaceae as inferred from nuclear CRABS CLAW sequences. Taxon 57: 434–451. – Probably still the best Fagaceae tree, and surely not a bad basis for probabilistic mapping of morphological traits in the family.

Manos PS, Cannon CH, Oh S-H (2008) Phylogenetic relationships and taxonomic status of the paleoendemic Fagaceae of Western North America: recognition of a new genus, Notholithocarpus. Madroño 55: 181–190. – the tree failed to resolve the monophyly of the largest genus, the oaks, but depicts well the data reality when combining ITS with plastid data and, hence, provides a good trade-off guide tree.

Please stop using cladograms!

I really like the journal PeerJ, not only because it is open access and publishes the peer review process, but also because it's one of the few that adhere to strict policies when it comes to data documentation. In my last (on my own) 2-piece post (part 1, part 2), I showed what networks could have offered for historical and more recent studies in Cladistics, the journal of the Willi Hennig Society. In this one, I'll illustrate why paleontology in general needs to stop using cladograms.

An example

In a recent article, Atterholt et al. (PeerJ 6: e5910, 2018) describe and discuss "the most complete enantiornithine from North America and a phylogenetic analysis of the Avisauridae". I'm not a paleozoologist and "stuff of legend", but their first 17 figures seem to make a good point about the beauty of the fossil and its relevance; and it is interesting to read about it. This makes me envy paleozoologists a bit — the reason I exchanged chemistry for paleontology was my childhood love for the thunder lizards; I specialized in zoology not botany for graduate biology courses, and I fell in love with social insects, especially bees; but then more general circumstances pushed me into plant phylogenetics.

The result of Atterholt et al.'s phylogenetic analysis is presented in their figure 18, as shown here.

Figure 18 of Atterholt et al. (2018): "A cladogram depicting the hypothetical phylogenetic position of Mirarce eatoni." [the beautiful fossil is highlighted in bold font]

This looks very familiar — graphs like this can be seen in many paleontological studies, not only those in Cladistics. However, this is a phylogeneticist's "nightmare" (but a cladist's "dream").

First, phylogenetic trees, especially those that were weighted post-analysis several times to get a more or less resolved tree, should be depicted as phylograms — trees with branch lengths. Phylogenetic hypotheses are not only about clades, and what is sister to what, but about the amount of (inferred) evolutionary change between the hypothetical ancestors, the internal nodes, and their descendants, the labelled tips. For example, we may want to know how long is the root of the clade (Avisauridae, Avisaurus s.l.) comprising the focus taxon compared to the lengths of the terminal branches within the clade. Prominent roots and short terminals are a good sign for monophyly (inclusive common origin), or at least a fossil well placed, whereas short roots and long terminals are not.

The above tree as phylogram (using PAUP*'s AccTran optimization). The beauty of cladistic classification is that the new specimen could have just been described as another species of Avisaurus (but read the author's discussion).

In this example, we seem to be on the safe side, although one may question the general taxonomic concept for extinct birds. Are the differences enough to erect a new genus for every specimen? This is hard to decide based on this matrix.

Second, a tree without branch support is just a naked line graph, telling us nothing about the quality (strengths and weaknesses) of the backing data. Neontologists are not allowed to publish naked trees. In molecular phylogenetics, we are not uncommonly asked by reviewers to drop all branches (internodes) below an arbitrary threshold: a bootstrap (BS) support value < 70 and posterior probability (PP) < 0.95. In palaentology, it has become widely accepted to not show support values at all. The reason is simple: the branch support is always low, because of data gaps and homoplasy. This is a problem the authors are well aware of:

The modified matrix consists of 43 taxa (26 enantiornithines, 10 ornithuromorphs) scored across 252 morphological characters [the provided matrix lists 253], which we analyzed using TNT (Goloboff, Farris & Nixon, 2008a). Early avian evolution is extremely homoplastic (O’Connor, Chiappe & Bell, 2011; Xu, 2018) thus we utilized implied weighting (without implied weights Pygostylia was resolved as a polytomy due to the placement of Mystiornis) (Goloboff et al., 2008b); we explored k values from one to 25 (see Supplemental Information) and found that the tree stabilized at k values higher than 12. In the presented analysis we conducted a heuristic search using tree-bisection reconnection retaining the single shortest tree from every 1,000 replications with a k-value of 13. This produced six most parsimonious trees with a score of 25.1. These trees differed only in the relative placement of five enantiornithines closely related to the Avisauridae, forming a polytomy with this clade in the strict consensus tree (Consistency Index = 0.453; Retention Index = 0.650; Fig. 18).

I've seen much worse CI and RI values in the paleophylogenetic literature (some of them are plotted in this post). For a phylogenetic inference, homoplasy equals internally incompatible signals — many characters show different, partly or fully conflicting, taxon bipartitions; or, in other words, they prefer different trees. The signal in the matrix is thus not tree-like — it doesn't fit a single tree. That's why we have to choose one using TNT's iterated reweighting procedures. (Note: an alternative "phenetic" Neighbor-joining tree has a computation time < 1s, and produces the same tree for the Ornithumorpha and the root-proximal, 'basal' part of the tree, except that Jeholornis is moved two nodes up; but it shuffles a lot in the Longirostravis–Avisauridae clade.)

Another point is that the more homoplasy we have, then the higher must have been the rate of change (here: visible anatomical mutation). The higher the rate of change, the higher the statistical inconsistency of parsimony.

In short, paleontologists (Atterholt et al. just follow the standard in paleophylogenetic publications) use data with tree-unlike signal to infer trees (see also David's last post on illogicality in phylogenetics) under a possibly invalid optimality criterion, which are then used to downweight characters (eliminate noise due to homoplasy) to infer less noisy, "better" trees.

The basic signal

We can't change the data, but we can explore and show its signal. And the basic signal from the unfiltered matrix is best visualized using a Neighbor-net splits graph.

Neighbor-net based on mean pairwise taxon distances. Thick edges correspond to branches in the published tree.

Some differentiation patterns that explain the clades in the tree can be traced, but it becomes difficult in the group that is of most interest: the (inferred) clade(s) comprising the newly described fossil. In the Neighbor-net this is placed close to another member of the Avisauridae, but not all. The matrix is not optimal for the task at hand.

The data properties

The matrix is a multistate matrix with up to six states in the definition line (although only five are used, as state "5" is not present). The taxa have variable gappyness (i.e. the proportion of completely undetermined cells), between 2% (extant birds: Anas and Gallus) and 94% (Intiornis, an Avisauridae) — the median is 56%, and the average close to it (54%). The "hypothetically" placed fossil Mirarce eatoni (in the matrix it is under its old designation: "Kaiparowits") lacks a bit more of the scored characters (61%). That may strike one as a lot, but note that the matrix has 253 characters! However, we may well ask: if I want to place a fossil for which I can score 99 characters, why bother to include another ~150 that tell me nothing about its affinity? (Note: paleobotanists struggle hard even to get such numbers, we usually have at best 50 characters.)

Its closest putative relatives, the Avisaurus s.l., lack 90% of the characters; leaving us with max. 25 characters supporting the relevant clade (assuming that the 10% are all found in Mirarce as well). Coverage is not much better in the next-closest relatives (phylogenetically speaking).

Data coverage in the phylogenetic neighborhood of Mirarce eatoni

The missing data percentage may have mislead the Neighbor-net a bit, because we will have fed it with unrepresentative or highly ambiguous pairwise distances. In the the network, the focus fossil comes close to Neuquenornis, the only other Avisauridae with some data coverage. Looking at the heat map below, we see that missing data is indeed a problem in this matrix — we have zero distances between several pairs that show different distances to the better-covered taxa.

The distance matrix drawn as a heat map: green = similar, red = dissimilar (values range between 0 and 0.8). Red arrows: taxa with too many (and ambiguous) zero pairwise distances.

The closest relative of Mirarce is, indeed, Avisaurus/Gettya gloriae, but the latter has zero distances to various other poorly covered taxa from the phylogenetic neighborhood, in contrast to the much better-covered Mirarce. Neighbor-nets are very good at getting the obvious out of a morphological matrix, but they don't perform miracles. However, why should we include poorly known taxa at all during phylogenetic inference? Wouldn't it be better to infer a backbone tree (or network showing the alternative hypotheses) based on a less gappy matrix, and then find the optimal position of the poorly known taxa within that tree (network)?

Estimating the actual character support

Some characters cover just 10–20% of the taxa, whereas others are scored for most of them — more than half of the characters are missing for more than half of the taxa. Using TNT's iterative weight-to-fit option means that we infer a tree, ideally one fitting the well-covered data (taxon- and character-wise), and then downweight all conflicting characters elsewhere to fit this tree. We then end up with a tree where we have no idea about actual character support. Since the matrix is a Swiss cheese, we only can re-affirm the first-inferred tree.

Let's check the raw character support, using non-parametric bootstrapping and maximum likelihood as the optimality criterion (corrected for ascertainment bias, as implemented in RAxML).

ML-BS Consensus Network (using Lewis' 2-parameter Mk+G model). Edge lengths are proportional to the BS support values of taxon bipartitions (= phylogenetic splits, internodes, branches in phylogenetic trees). Only splits are shown that occurred in at least 10% of 900 BS pseudoreplicates (number of necessary BS replicates determined by the Extended Majority Rule Bootstrap criterion), trivial splits collapsed. Thick edges correspond with branches in Atterholt et al.'s iterative parsimony tree; coloring as before.

The ML bootstrap Consensus Network bears not a few similarities to the distance-based Neighbor-net. The characters do not support the Avisauridae subtree, as depicted in the published TNT tree, but there are faint signals associating some of them to each other, despite the missing data. Keep in mind: a BS support of 20 for one alternative and < 10 for all others means (ideally) one fifth of the characters support the split, and the rest have no (coherent) information. Some sister pairs have quite high support (for this kind of data set), and Gettya gloriae is resolved as sister of Mirarce (unambiguously, with a BS support = 67). But, the matrix hardly has the capacity to resolve deeper relationships within the group of interest, the Enantiornithes — the polytomy with the next relatives seen in the tree and the corresponding clade dissolve. This confirms what we saw in the Neighbor-Net (despite missing data distortion).

The matrix and the tree show something that could have been deduced directly from the distance matrix: the poorly known Gettya (Avisaurus) gloriae is (literally) the closest relative of the enigmatic new genus / species Mirarce (morphological distance of 0.08 compared to 0.1–0.64 for all other taxa). But is this overall similarity enough to conclude Avisaurus, Gettya and Mirarce are a monophyletic group within the Avisauridae?

What the authors (and all paleontologists doing phylogenetics) should have done

(I would have skipped all trees, naturally, but peer reviewers and most readers probably need to see them.)

• Trimmed the matrix to include only those characters preserved in the fossil of interest, in order to minimize missing data artefacts during inference.
• Shown the Neighbor-net to visualize the primary signal situation, including and excluding poorly covered taxa. From the Neighbor-net it is already obvious that the fossil is an Enantiornithes, so any subsequent optimization / inference could have focussed on this group alone.
• Then inferred a backbone tree excluding poorly covered taxa, and shown the resulting phylogram. In case one needs to test the Enantiornithes root (the Neighbor-net gives us two alternatives for the Enantiornithes root: Pengornis + Eopengornis or Protopteryx + Iberomesornis), there is no point in including the poorly covered Enantiornithes or the worst-covered taxa outside this clade.
• Then optimized the position of the poorly covered taxa in the backbone tree. I recommend using RAxML's evolutionary placement algorithm (EPA) for this, but you can also do this in a parsimony framework if you wish. (EPA can also be used to test outgroup roots: here, one would search the branch at which all non-Enantiornithes fit best.)
• Shown the resulting phylogram including all taxa — that is, read in the topology to the analysis, and then re-optimize branch lengths.
• Shown a Support Consensus Network to illustrate the support for the branches in the preferred tree and their competing alternatives. (There may be one or more, as there are many options to estimate branch support.) How sure can we be about relationships within the Avisauridae and their relationships to other Enantiornithes?

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Postscriptum. For those who are curious about how the ML tree would look like, here it is:

I have no idea about birds, but from a methodological point of view this is an equally (if not more, because unforced) valid hypothesis for the data set. And demonstrating its limitations: note the relatively long branches with very low support making up the backbone of the Enantiornithes clade. This is typical for matrices lacking coherent discriminatory signal and/or struggling with internal conflict.

More on networks for placing fossils, such as Eocene lantern fruits

A colleague pointed me to a paper published last year in Science about a spectacular fossil find: an Eocene Physalis-fruit with a preserved lampion. In an recent post, I advocated Neighbor-nets as nice and quick tools to place fossils phylogenetically. In this post, I'll will exemplify this once more, and argue why this would have been even more informative than what the authors showed as graphs.

The study and the data

In their 2017 paper, Wilf et al. (Science 355: 71–75) describe a new fossil find, which, by itself, rejects the often-too-young molecular dating estimates for Solanceae, the potato-tomato family, the "Nightshades". The Nightshades include many well-known plants, in addition to potato/tomato (the latter is phylogenetically a subclade of the potatoes) — we have e.g. the tobacco genus (Nicotiana), and also the genus Physalis, which includes several species commercialized as fruits (e.g. P. peruviana, also known as Cape gooseberry or goldenberry) and ornamental plants (e.g. P. alkekengi, the Chinese Lantern).

Just by looking at the pictures showing the fossil (Wilf et al.'s text-Fig. 1), anyone who ever ate a physalis, would agree that it was produced by a member of the genus. However, science is not usually about common sense, but about formal reconstructions. Thus, the authors placed their fossil using a total evidence tree approach: they scored 13 morphological traits as binary or ternary characters, concatenated these data with a molecular data set and inferred trees under maximum parsimony (their text-Fig. 2, below) and maximum likelihood (the tree can be found in the supporting information).

Wilf et al.'s total evidence tree showing the (quoted from the legend)
"Phylogenetic relationships of Physalis infinemundi sp. nov. and selected Solanaceae species" (their Fig. 2). Strict consensus of 2835 most parsimonious trees of 3510 steps (CI = 0.438, RI = 0.726)."

Based on the graph, one can confirm that the fossil (arrow; pictured, too) is part of the core Physalis, but its position within this core clade is unresolved. The Decay index shown indicates that moving the entire branch would require just one step more. Not overly re-assuring regarding the total length of the tree (3510 steps) and underlying data (the used matrix has 7070 characters!)

The molecular data were selected from an earlier study (Särkinen et al., BMC Evol. Biol., 2013), but the total evidence matrix is not provided (see this post on why we want to publish our phylogenetic data). But at least the "...morphological matrix developed in this paper is tabulated in the supplementary materials."

This file includes two sheets: the first shows the "raw scores", including four continuous characters, and the second shows the "character scoring" used for the analysis, where the continuous characters were scored (binned) as ternary and binary characters. The iinformation provided is partly wrong, likely to be the result of copy & paste errors (this is another reason why it should be obligatory for phylogenetic studies to provide the data as aligned-FASTA or NEXUS file). A corrected version of the "character scores" sheet based on the "raw scores" sheet is included in the figshare submission for this post.

By just filtering this matrix for same-as-in-the-fossil characters, we can identify two extant species that are identical to the fossil in all scored characters: Physalis acutifolia and P. lanceolata. Both are part of the Physalis core clade in Wilf et al.'s total evidence tree, but their position is as unresolved as that of the fossil.

Enlarged part of the above figure, showing the absolute character difference (0 to 5 out of 13 covered characters) between the fossil and other members of the Physalis core clade.

The reason for this becomes clear in the total-evidence maximum-likelihood tree. Here, the fossil is resolved as the sister of P. lanceolata (maximum likelihood bootstrap support: ML-BS < 70, the actual value would have been nice), to which it is identical, both being deeply nested in the Physalis core clade. However, the other identical species (morphologically), P. acutifolia, is placed in the first diverging subclade of the core clade (ML-BS < 70, along with most of the backbone of this clade). The "low" support may have two possible reasons:

• the fossil, with 99.8% missing data, acts as a 'rogue' taxon; or
• the genetic data provides little discriminating or ambiguous signals.

Solanaceae genera can be tricky, and the gene sample lacks high-divergent sequence regions. Since the molecular data are not documented, I can't assess how significant this separation is, but it appears to be supported by at least some mutations: the tree-wise distance is about 0.04 expected substitutions; and the two morphologically indistinct (regarding the scored characters) species are genetically distinct (to some degree).

Extract from Wilf et al.'s Fig. S1, showing the Physalinae subtree with the core Physalis clade and the deeply nested fossil P. infinemundi (in bold font). Support is only shown for branches with a ML-BS support ≥70.

Trees may fail to show the obvious, but networks won't

Just by using the Neighbour-net to visualize the signal in the morphological partition, we can directly argue that the fossil is likely to be part of the core Physalis. Thus, being Eocene of age, rejects the much-too-young age estimates in e.g. the dated tree by Särkinen et al. (the reference for the molecular data used by Wilf et al.)

Neighbour-net splits graph based on the morphological data partition included in Wilf et al.'s "supermatrix".

In contrast to the little information that comes along with the tree shown above (soft-ish polytomy, weak Decay index, potentially decreased ML-BS support), the splits graph highlights the ambiguity (incompatibility) of the morphological signal. The graph shows little tree-likeness, and members of the same (sub)tribe show little coherence (C = Capsiceae, H = Hyoscyameae, J = Juanulloeae, S = Solaneae; W = Withaninae; all represented by de-facto molecular clades with ML-BS ≥ 77 in Wilf et al.'s supplement Fig. S1). There is one notable exception: members of the core Physalis (red dots) are sufficiently distinct from anything else, forming a highly supported clade (ML-BS = 98 in Wilf et al.'s fig. S1),.

The network also shows that the fossil is identical to both P. acutifolia and P. lanceolata.

Neighbour-net after reducing the taxon set to the phylogenetic neighbourhood of the fossil specimen. Filled fields indicate sister/sibling species supported by a ML-BS >= 80 in Wilf et al.'s "total evidence" ML tree.

By focusing on the phylogenetic neighborhood of the fossil, we end up with a spider-web-like graph. Which means that the morphological partition has little consistent signal for recognizing potential relatives: the same features are likely to have evolved in parallel (all members of this neighborhood a likely to share a common origin) — 50 million years (and more) is a long time for a lineage to end up with a similar fruit (see also the maximum-parsimony character reconstructions on the parsimony strict-consensus tree provided in the supplement to Wilf et al.'s study).

Data and graphs

The Splits-NEXUS files for the Neighbor-nets and NEXUS-versions of Wilf et al.'s Data S1, as well as additional graphics (network with labeled bubbles) can be found on figshare.

Want to place a fossil in a minute? Just use Neighbour-nets

Palaeontological phylogenetic researchers typically put a lot of effort into inferring trees. It has been argued (and occasionally pointed out during manuscript reviews) that only by placing a fossil in an explicitly phylogenetic framework can we assess what it represents. I sympathize with this notion, but in most cases we don't need any elaborate analysis to do it — a quick network-based analysis will do the trick.

In this post, I'll demonstrate my point using the most recent matrix presented by two eminent plant morphology veterans. In a fresh-off-the-press paper, James Doyle & Peter Endress provide a "Phylogenetic analysis of Cretaceous fossils related to Chloranthaceae and their evolutionary implications" (Botanical Review) using their morphology matrix focussing on early diverging angiosperm lineages, which was originally used for a paper by Sareela et al. (Nature 446: 312–315, 2009) and has been continually updated.

Like all morphological matrices that aim to cover as much as possible, Doyle & Endress' matrix does not provide any strong tree-like signal, and hence it has little use for inferring phylogenetic trees. Doyle & Endress deal with this issue by using a (more or less molucular-based) backbone tree enforcing several clades for the modern taxa, and then trying to find the most parsimonious placement of the fossil(s). This approach works to some degree but has two problems: one theoretical and one practical.

First, the backbone tree, or any molecular-informed topology, is usually some steps longer than the most-parsimonious trees that could be inferred on their matrix. In other words, morphological evolution in plants doesn't fully fulfill Ockham's Razor. Why should this also be the case for the fossils?

Second, moving a fossil through the branches to find the best-placement takes some time, and will lead to many equally parsimonious solutions. Not rarely, the fossil can be placed on quite distant branches, producing trees that are only a few steps longer.

A graph I made depicting the 'parsimoniousness' of placing a fossil, Monetianthus (a Cretaceous water lily), within a given topology using an earlier version of Doyle & Endress' matrix (fig. 7 in Friis et al., Int. J. Plant Sci., 2009). The number of additional steps was estimated by moving the target taxon, the fossil, to the accordingly coloured branch of the tree. (PS To show that the fossil is a water lily, a Nympheaceae, we used a Neighbour-net)

For Doyle & Endress' papers this is no big problem, because they just show the best placements as well as those a few steps longer. For example:

Placing the Chloranthistemon species on the stem lineage of Sarcandra and Chloranthus is four steps less parsimonious than placing them on the stem of Chloranthus. For perspective, only two steps are added if the Asteropollis plant is moved to the stem of the whole family. If a four-step parsimony debt is accepted in moving Chloranthistemon to a morphologically less favored position, one may ask why the Asteropollis plant is considered a reliable minimum age constraint for the family.

But with respect to the fact that morphological evolution is not necessarily parsimonious, and that even the modern taxa can show variable root to tip pathlength distances, I always remain skeptical of this approach.

A Bayesian-inferred angiosperm tree based on a total-evidence matrix, built from a curated version of Soltis et al.'s 2011 matrix and including the 2010-version of Doyle & Endress' matrix as morphological partition (provided as open data @ figshare). Note that many fossils (Cretaceous, ~100 Ma) have longer terminal branches than their surviving relatives (hence, made Bayesian total evidence dating impossible).

Aside from this, the matrix signal is pretty straightforward when it comes to decide on the potential position of the fossil in the angiosperm part of the Tree of Life. And the analysis takes (literally) moments.

You just take the matrix, calculate mean pairwise morphological distances (done in a blink), export the distance matrix as NEXUS-formatted file and input this to SplitsTree, which will give you a Neighbour-net (in another blink).

A Neighbour-net based on Doyle & Endress' 2018 matrix including only the modern-day taxa.

Most members of the well-established clades, main angiosperm lineages, cluster in the Neighbour-net (bracketed names point to somewhat scattered clades). In case the signal from a fossil is trivial, it will be nested within the respective cluster. Trivial signals are when a fossil has a character suite that indicates it is much more similar to one of the clusters than to any other, which usually means that it is part of the same evolutionary lineage. Convergences may be common, and characters homoplasious, but evolving the exact same suite of characters while not sharing common ancestry is quite unlikely.

The Neighbour-net including the matrix' fossils. Note that the relative position of the Eudicots has changed and Circaeaster and Euptelea are placed closer to the other Ranunculales, although the pairwise distances between all modern taxa have not changed. The re-arrangement is solely a fossil-inclusion effect. By adding fossils attracted to Ceratophyllum, this enigmatic and isolated genus is drawn away from the most basal eudicots.

Two of the fossils apprear to have unique character suites, placing them intermediate between two phylogenetically isolated plants, the unique Amborella (still considered the earliest branching modern-day angiosperm; one species on New Caledonia) and Ceratophyllum, an equally enigmatic water plant. The remainder are clearly members of the Chloranthales.


Having identified the phylogenetic Neighbourhood of the fossils, we can then focus on this neighbourhood (in SplitsTree: Select the comprising OTUs; then go to menu Data > Keep only selected taxa).

The Neighbour-net after all non-neighbourhood OTUs have been removed.

From this graph we can directly conclude:

• The Asteropollis plant is a close relative, likely a sister or early representative, of Hedyosmum.
• Couperites represents an early and substantially diverged lineage within the Chloranthales — its closest living relative appears to be Ascarina, next to Hedyosmum the most derived living Chlorantales (here: one would need to see if there is any shared character suite).
• Zlatkocarpus is an ancestral form of the Chloranthales core clade, comprising Ascarina and the sister taxa Chloranthus and Sacandra (one would need to check the possibility that this could be a missing data artefact).
• Canrightia and Canrightiopsis are sister lineages or precursors of Chloranthus and Sacandra (see the open access tree-and-network-based paper by Friis et al. 2015, Grana 54: 184–212)
• The Pennipollis plant is an ancient isolated Chloranthales lineage, with no living relative.
• Appomattoxia and Pseudoasterophyllites may be (very) distant relatives of Ceratophyllum, the latter an isolated genus that has long been and still is a problem for molecular phylogenies. Alternatively, they may represent early and extinct angiosperm lineages (or the same lineage) with no modern counterparts.

To say anything beyond this based on the current data set quickly leaves the grounds of objectivity, and requires a priori assumptions about the importance of certain morphological traits being shared or not (i.e. not expressed, not just missing due to poor preservation).

[For those interested in a formal discussion of these results, see Doyle & Endress, 2018, pp. 7–25.]

To refine the analysis, we can just reduce the character set to the characters scored for the fossils.

A Neighbour-net based on distances computed using a character-subset generated by excluding all invariable characters (in PAUP*: Exclude constant) for the taxa included in the network (66 characters, including eight not defined for any fossil taxon). Grey depicts a (molecular-data backed) tree hypothesis that could explain the seen differentiation pattern

To take the next step, morphological matrices alone will have no practical use, because they will not allow us to identify fast vs. slow evolving traits and lineages. A lineage that goes through bottlenecks or colonizes new niches will be genetically, and morphologically, more distinct than one that remained in calm waters. One could map the preserved traits found in each fossil onto a molecular tree, and include the information about actual branch lengths in that tree to put forwards hypotheses about the ancestral state (e.g. Mendes et al., Grana 53: 283–301 [open access] for Lardizabalaceae), and possibly even time the divergences. This would enable one to compare the situation in the fossils with the top-down hypotheses about morphological evolution for the very same time period.

But that would be mostly tree-based analyses, and thus nothing for a Genealogical World of Phylogenetic Networks post.

Data — In case you are interested in the primary data matrix, a ready-to-use NEXUS version and the raw Split-NEXUS files have been uploaded to figshare.

A (wal)nut to crack – what a network tells you that no tree can

In this post, I will show a network that I generated some time ago as illustration of a point: morphological data should not be used to infer trees, but networks, instead — especially when the goal is to place some fossils in a modern-day phylogenetic framework.

In 2007, Manos et al. (Systematic Biology 56:412–430) published an interesting phylogenetic study that provided a phylogenetic framework to place some enigmatic fossils of the Juglandaceae, the walnut family. Following my preferred procedure (presumably without realizing it), they recruited a palaeobotanical expert to erect a morphological partition.

Given the high quality of the matrix, this is an ideal example to demonstrate the utility of networks in (palaeo)phylogenetic research and to discuss the question of potential ancestor-descendant relationships, and their poor representation in trees (especially cladograms). Phylogenetic relationships within modern Juglandaceae are relatively well resolved. Rhoiptelea, a relict genus found in the mountains of northern Vietnam and south-western China, is sister to the remainder of the family — it is now subfamily Rhoipteleoideae, but was traditionally its own family. Rhoiptelea is an living fossil: flowers with fitting in-situ pollen and seeds have been found in the Late Cretaceous (Heřmanová et al. 2011, IJPS 172: 285–293; cryptically named Budvaricarpus serialis, the "Serial Budvarseed", because one is not allowed to use a modern-day genus for naming a 85–90 million year old angiosperm, even when it looks the same). The remainder of the Juglandaceae falls into two main clades, recognized as subfamilies:

1. the Juglandoideae — the walnuts (Juglans) and their closest relatives: the (eastern) North American-East Asian disjunct genus Carya, the Eurasian relict genus Pterocarya (mainly Transcaucasia, East Asia), and the monotypic genera Cyclocarya and Platycarya.
2. the Engelhardioideae — a group of tropical-subtropical, mostly relict genera: Alfaroa + Oreomunnea in the equatorial regions of the New World; and South East Asian-Malesian genus Engelhardia and the, probably monotypic, Alfaropsis widespread in China (sometimes still included in Engelhardia; e.g. current Flora of China, despite unambiguous molecular and morphological evidence).

Juglandaceae produce (winged) seeds and pollen that are relatively easy to identify. They are well-known and very common companions of palaeontologists during much of the Cenozoic, especially the (today geographically very restricted) Engelhardioideae. But in addition to the modern genera, the family includes some very interesting, unique fossils — the idea is to place these in a phylogenetic framework.

Results of the study of Manos et al. (2007).
Arrows indicate the position of the fossils. a) A majority rule consensus cladogram using a cut-off of 50 based on the morphological partition; b) the total evidence counterpart.

As can be seen from the above trees (taken from the paper), morphology reflects some of the molecular phylogenetic relationships — the Juglandoideae are supported as a clade, as are most genera (except for Engelhardia and Oreomunnea). Two fossils, Pal(a)eoplatycarya and Platycarya americana were resolved as sister taxa to their modern counterpart, Platycarya strobilacea; and the two enigmatic fossils Polyptera (the "many-winged one") and Cruciptera (the "cross-winged one") could be associated with the Juglandoideae. The total evidence approach indicated that Cruciptera is part of the "crown-group" Juglandoideae, in contrast to Polyptera, that appears at a more "basal" (root-proximal) position in this subclade. A sixth fossil, Pal(a)eooreomunnea could not be resolved with certainty (placed as sister to all Juglandoideae in the total evidence tree). As the name indicates, literally the "Ancient Oreomunnea", we would have expected it to group with the Engelhardioideae, which form a clade in the total evidence tree.

This is okay so far as it goes but, beyond potential sister relationships, these cladograms show very little. When I place a fossil such as Cyclocarya in the phylogeny, I would like to know whether it is more closely related to Juglans, Pterocarya or Cyclocarya. Is it an early sister lineage of all of these, or even a precursor? Cladograms cannot answer such questions.

The persistent issue of pseudo-clades

It has been pointed out in earlier posts that clades/grades are not necessarily synonyms of Hennig's concepts of monophyly and paraphyly, mainly because of convergent evolution creating data splits that are incongruent with the true tree. Parsimony-based analyses are especially vulnerable, because each change represents a step to be optimized.

One alternative method to place fossils in a (molecular-based) phylogenetic framework is the evolutionary placement algorithm (EPA; Berger & Stamatakis 2010, AICCSA conference paper). This changes to a probabilistic framework, and queries each fossil alone using its morphological partition but using the molecular-based tree as framework.

Summarized result of the evolutionary placement algorithm as implemented in RAxML.
The number represents a probability to join the fossil at the according branch using maximum likelihood as optimality criterion.

This gives the above tree as the result for the Walnut data set. Palaeooreomunnea is now unambiguously linked to one of the two included species of Oreomunnea, O. mexicana. Cruciptera is associated (again unambiguously) with Cyclocarya. Furthermore, not only are Palaeoplatycarya and the extinct North American Platycarya relatives of the modern-day Platycarya, but also Polytera. This, according to the original analysis, is the first-branching member of the remainder of the Juglanoideae, ie. all genera except Platycarya.

And the network shows us why

The most important problem with morphological data sets is that their signals are complex, and usually not very tree-like. Hence, whenever we optimize fossils along a tree (either by directly analyzing the morphological data or by some form of total evidence approach), the analysis has to fit in this odd little OTU at all cost, even when it means collapsing an entire clade. Simultaneous optimisation of two or more fossils triggers further branching artifacts, and may decrease branch support, because we have no molecular data compensating for eventual branch attraction conflicting with the actual phylogeny.

Let's take the Polyptera as an example. If we de-root the trees, the original total evidence placement and the ML-EPA are not that different from each other: Polyptera is just moved one node. A easily inferred Neighbour-net, which is not 1-dimensional like a phylogenetic tree, but 2-dimensional, shows the reason why (and only by using the morphological data partition).

The neighbour-net based on the Manos et al.'s morpho-data partition.
Numbers at branches represent nonparametric boostrap support (Least-squares and Maximum parsimony criteria) and Bayesian posterior probabilities.

• We can see that Polyptera has a unique morphology (it shows the longest terminal edge of all fossils), making it equally similar to Platycarya and the remaining Juglandoideae: Juglans, Pterocarya, Cyclocarya, and Carya (Annamocarya is a not-widely-accepted Chinese genus, genetically indistinct from other East Asian Carya). This explains its instability in tree-based reconstructions. Assuming that Rhoiptelea points to the actual root, one could use the relatively high branch support values as an argument to say that Polyptera evolved after Platycarya split from the remainder of the Juglandoideae. But the network shows that the signal is not that straightforward, and Polyptera may just be a third lineage within the Juglandoideae (note the short orange edge bundle in contrast to the large red and green ones). A crucial question to check, also regarding the ML-EPA result, is whether the orange-edge clade (including Polyptera) is supported by uniquely shared characters and not just a tree-branching artifact because of the distinctness of the Platycarya group. Being substantially distinct (genetically and morphologically) from the remainder of the Juglandoideae, they must be placed as sister taxa. Being a fossil Polyptera is not that distinct, hence, placed in the Juglandoideae core clade. Distance-based and parsimony methods are more vulnerable to long-branch attraction (or short-branch culling) than is ML; and Bayesian analysis optimizes to a tree best comforting all signals in the data (compatible or not).
• Cruciptera is more similar to Cyclocarya and Pterocarya than to Juglans, and represents a more primitive (ancestral) form. Based on the position of Cyclocarya and Pterocarya, we can directly conclude that they are morphologically less derived than Juglans, their sister taxon. Hence, one should be careful interpreting Cruciptera as a precursor of eg. Pterocarya, but would have to go back into the matrix and assess which characters differentiate within this part of the graph, in order to decide whether the similarity between them is a genuine representation of shared (common) origin, and not just due to symplesiomorphies.
• The fossil counterparts of modern-day Platycarya span a quite prominent box-like structure in the network, but the blue edge has little support from tree-based analyses. A simple explanation would be that these two more ancient members of the Platycarya lineage, and are less derived than their modern counterpart and the other Juglandoideae.
• Palaeooreomunnea is placed as one would expect for an ancestral form of the Engelhardoideae. It is clearly closer to the New World pair Alfaroa and Oreomunnea than to the Old World Alfaropsis and Engelhardia.

Data & software for EPA

The data matrix that I used for the ML-EPA, the Neighbour-net and the competing branch support analyses can be found in the supplementary information of the original paper.

EPA is implemented in RAxML since Version 7 and usually used to place environmental short sequence reads (Berger et al. 2011, Syst. Biol. 60:291–302). For a published application of EPA to place fossils, see e.g. Bomfleur et al. 2015, BMC Evol. Biol. 15:126.