How I got my get-go together with only co-authorship inwards Nature
End 2006 (or start of 2007), I was offered a co-authorship on a newspaper that got stuck inwards Nature’s Impermeable Fog (we never managed to acquire whatever newspaper into that exceptional fog at all, whatever nosotros dared to submit to Nature or Science was rejected inside 24h). The newspaper (Friis et al. 2007) was nigh an enigmatic Cretaceous seed studied amongst an extremely sophisticated non-destructive imaging method. But this alone, together with the substantial fame of the authors already on the paper, was non plenty to acquire it through. One of the Wizards of the Forest (i.e. an anonymous peer) found the newspaper needed an explicit phylogenetic analysis (it didn't, but thank y'all to this opinion, I was funded for 4 years yesteryear the Swedish state). The get-go author, non trusting anyone else, asked a colleague, whether he could arrive at it (she knew he had done it inwards the yesteryear for 1 of his papers). He answered that he leaves this employment organization solely to his trusted High German analyst, me. So, I got a matrix scoring for morphological characters that had been used to infer trees of extinct together with extant seed plants (spermatophytes; Hilton & Bateman 2006), together with the seed was included. I made the required analysis (classic parsimony tree together with bootstrapping analysis), irksome but plenty to acquire a co-author seat. |
| In-text figure 3, my visible contribution to the Nature paper |
Non-trivial information demand non-established procedures, right?
I idea so. My contact amongst phylogenetic networks (in the broadest sense) was relatively fresh, but I remove idea that a matrix amongst a lot of signal issues – aside the commons missing information problems, incompatible signals, many homoplastic characters – is only the correct cloth for them. So, I did non only create a tree amongst some branch back upwardly annotated along the branches (which y'all tin honor inwards the Supplementary Information to the paper). Instead, I generated consensus networks to summarise the sample of as (most) parsimonious trees together with the bootstrap (pseudoreplicate) tree samples; together with I used the matrix of pairwise distances inferred from the grapheme matrix to generate a neighbour-net splits graph, a planar, i.e. 2-dimensional ‘meta-phylogenetic’ network (Bryant & Moulton 2002; Bryant & Moulton 2004) [Bryant & Moulton called it a phylogenetic network, together with I did, too, until David Morrison pointed me to his post, together with he’s correct that nosotros should non telephone vociferation upwardly splits graphs phylogenetic networks.] |
| A neighbour-net of extinct (ancient) together with modern seed plants, peradventure the most- viewed unpublished figure I ever made. Main lineages are coloured, the earliest precursors ('progymnosperms') together with ancient, real primitive 'seed ferns', the conifers (needle trees) together with their precursors together with ancient relatives (Cordaitales), Ginkgo, cycads together with to a greater extent than advanced Mesozoic seed ferns, together with finally the crown-groups: the today-dominating flowering plants (angiosperms) together with the 'BEG clade' including extinct, ± derived groups (Bennettitales, Erdmanithecales), the seed nosotros placed, together with the modern-day Gnetales. |
Possibly the get-go of its form using such data. My get-go writer liked what she saw, together with so did essentially every other mortal I showed it to, so together with inwards the many years to come upwardly (I showed it effectively to every scientist I met, together with quite a number of non-scientists I entertained amongst the background story). But the 2nd writer was wary that such openly “phenetic” methods could give the Wizards the concur to plough downwards the newspaper (he used his famous catch-phrase, when nosotros discussed it: “I wouldn’t arrive at that”, which translates into “no”). Back inwards the days many people toying some amongst phylogenetics (particular botanists, and, notoriously, palaeontologists) had plainly non read Felsenstein’s (2004) majority Inferring Phylogenies and yet considered all distance-based analysis as “phenetic” inwards contrast to the “phylogenetic” parsimony (and maximum likelihood or Bayesian inference, if y'all must role them…) The same people lost the ‘Phylogenetic War’ a decade earlier (see chapter 10 inwards Felsenstein’s book), but this didn’t hateful they could non honor someone else to selection on. So, when the revision was submitted to Nature, my dear figure was non fifty-fifty inwards the Supplementary Information. [I learned a few other things nigh high-impact publications, which I may percentage some after signal inwards the correct context.]
 |
| The figure, as it should convey appeared inwards the Supplementary Information, before the veto of the 2nd author |
The lost graph: a network based on similarity amid extinct together with extant spermatophytes
In spite the data-inherent problems amongst the underlying matrix (Hilton & Bateman 2006), the graph nicely depicts the actual relationships of the primary extinct together with extant phanerogam groups to each other, most of which yet stand. It furthermore illustrates the signal strengths together with weaknesses of the matrix. The angiosperms, the flowering plants – today’s most dominant together with various works life grouping – are recognised as a most distinct group, amongst only 1 possible closest fossil relative: Caytonia, a Mesozoic seed fern together with apparently a coding artefact. By severe matrix recoding Rothwell, Crepet & Stockey (2009) together with Rothwell & Stockey (2016) were able to dissociate that piddling bastard from the long-branching flowering plants. The circular scheme reflects the development from primitive forms (colloquially known as “seed ferns”) to increasingly modern together with complex ones (modern conifers, Gnetales together with angiosperms). Any human relationship inwards the master tree is found inwards the graph, as good as non so unlikely alternatives. Primitive members of each primary lineage are placed closer to the centre or putative root of the graph than derived ones. Also, the graph is the most comprehensive together with honest depiction of the signal inwards the underlying data, something that dorsum so my 2d author, the unsafe peer, together with – nearly 10 years after – also Rothwell & Stockey (2016) yet reject to realise: the signal is complex, together with cannot live captured yesteryear a unmarried tree (see also Coiro, Chomicki & Doyle 2017; together with this postal service on the topic). |
| Some to a greater extent than figures I made in course of teaching of the study. Left, a back upwardly consensus network based on parsimony bootstrapping. On the right, a consensus network of distance-based trees generated yesteryear eliminting 1 taxon per tree (both going – at the fourth dimension – likewise far into unchartered territory to live considered for the supplement) |
Epilogue
Two years later, I managed to pose out my get-go morphology-based networks (Denk & Grimm 2009; Friis et al. 2009), naturally inwards low/mid-impact journals, where they quite smoothly passed the wary eyes of Wizards of the Forest (and objections of surely co-authors). One or 2 pointed out that it is a “phenetic” analysis (which it is not, together with I told them so inwards our responses), but beyond that commutation critique the graphs were likewise alien to our peers that they dared to criticise them inwards to a greater extent than exceptional (and the editors had no argue or correct to object). And forthwith that I’m gratis to arrive at what I desire to, I’ve wrote a couplet of spider web log posts on David Morrison’s Genealogical World of Networks blog promoting the role of networks (planar or other) when studying morphological information sets. Our papers including them (Friis et al. 2009, 2015; Schlee et al. 2011; Grímsson et al. 2014; Mendes et al. 2014; Bomfleur, Grimm & McLoughlin 2015, 2017) are all quite good picked upwardly yesteryear the community (regarding number of downloads together with citations), together with nosotros volition run into if this helps to interruption downwards the wall inwards the heads.However, I can’t halt thinking: What if my graph would convey been published dorsum so inwards high-fly Nature? I peradventure would non convey to write those posts at all, because it would already live a criterion approach that long could convey replaced the commonly telling-nothing, oft severely biased strict consensus trees inwards nearly every morphology-based phylogenetic newspaper on extinct works life or brute groups published so far...
More posts on morphological data, fossils together with networks (including links to CC-BY-licenced figshare material)
Spermatophyte networks
Grimm GW. 2017. Should nosotros infer trees on treeunlikely matrices? In: Morrison DA, editor. The Genealogical World of Phylogenetic Networks. http://www.rachelteodoro.com/search?q=one-date-that-is-missing-in-manyGrimm GW. 2017. Morphology-based neighbour-net of seed plants. figshare. https://doi.org/10.6084/m9.figshare.5111062
Grimm G. 2017. Morphology-based neighbour-net of seed plants: quick exploratory information analysis of the matrix of Rothwell & Stockey (2016). figshare. https://doi.org/10.6084/m9.figshare.5143732
Related networks
Grimm GW. 2017. Stacking neighbour-nets: ancestors together with descendants. In: Morrison D, editor. The Genealogical World of Phylogenetic Networks. http://www.rachelteodoro.com/search?q=one-date-that-is-missing-in-manyGrimm GW. 2017. Stacking neighbour-nets: a real-world example. In: Morrison D, editor. The Genealogical World of Phylogenetic Networks. http://www.rachelteodoro.com/search?q=one-date-that-is-missing-in-many
Grimm GW. 2017. Osmundales diverstity through time: stacking networks. figshare. https://doi.org/10.6084/m9.figshare.5255014
Grimm GW. 2017. More non-treelike information forced into trees: a glimpse into the dinosaurs. In: Morrison D, editor. The Genealogical World of Phylogenetic Networks. http://www.rachelteodoro.com/search?q=one-date-that-is-missing-in-many.
Grimm GW. 2017. Networks, non trees, position “weak spots” inwards phylogenetic trees. In: Morrison D, editor. The Genealogical World of Phylogenetic Networks. http://www.rachelteodoro.com/search?q=one-date-that-is-missing-in-many
Grimm G. 2017. Classification of mosasaurs - using networks. figshare. https://doi.org/10.6084/m9.figshare.5497903
References
Bomfleur B, Grimm GW, McLoughlin S. 2015. Osmunda pulchella sp. nov. from the Jurassic of Sweden—reconciling molecular together with fossil bear witness inwards the phylogeny of modern regal ferns (Osmundaceae). BMC Evolutionary Biology 15:126.
Bomfleur B, Grimm GW, McLoughlin S. 2017. The fossil Osmundales (Royal Ferns)—a phylogenetic network analysis, revised taxonomy, together with evolutionary classification of anatomically preserved trunks together with rhizomes. PeerJ 5:e3433. https://peerj.com/articles/3433/.
Bryant D, Moulton V. 2002. NeighborNet: an agglomerative method for the construction of planar phylogenetic networks. In: Guigó R, together with Gusfield D, eds. Algorithms inwards Bioinformatics, Second International Workshop, WABI. Rome, Italy: Springer Verlag, Berlin, Heidelberg, New York, p. 375-391.
Bryant D, Moulton V. 2004. Neighbor-Net: An agglomerative method for the construction of phylogenetic networks. Molecular Biology together with Evolution 21:255-265.
Coiro M, Chomicki G, Doyle JA. 2017. Experimental signal dissection together with method sensitivity analyses reaffirm the potential of fossils together with morphology inwards the resolution of seed works life phylogeny. bioRxiv DOI:10.1101/134262.
Denk T, Grimm GW. 2005. Phylogeny together with biogeography of Zelkova (Ulmaceae sensu stricto) as inferred from leafage morphology, ITS sequence information together with the fossil record. Botanical Journal of the Linnéan Society 147:129–157.
Denk T, Grimm GW. 2009. The biogeographic history of beech trees. Review of Palaeobotany together with Palynology 158:83–100.
Friis EM, Crane PR, Pedersen KR, Bengtson S, Donoghue PCJ, Grimm GW, Stampanoni M. 2007. Phase-contrast X-ray microtomography links Cretaceous seeds amongst Gnetales together with Bennettitales. Nature 450:549–552.
Friis EM, Pedersen KR, von Balthazar M, Grimm GW, Crane PR. 2009. Monetianthus mirus gen. et sp. nov., a nymphaealean blossom from the early on Cretaceous of Portugal. International Journal of Plant Sciences 170:1086-1101.Friis EM, Grimm GW, Mendes MM, Pedersen KR. 2015. Canrightiopsis, a novel Early Cretaceous fossil amongst Clavatipollenites-type pollen span the gap betwixt extinct Canrightia and extant Chloranthaceae. Grana 54:184–212.Grímsson F, Zetter R, Halbritter H, Grimm GW. 2014. Aponogeton pollen from the Cretaceous together with Paleogene of North America together with West Greenland: Implications for the root together with palaeobiogeography of the genus. Review of Palaeobotany together with Palynology 200:161–187.
Hilton J, Bateman RM. 2006. Pteridosperms are the backbone of seed-plant phylogeny. Journal of the Torrey Botanical Society 133:119-168.
Mendes MM, Grimm GW, Pais J, Friis EM. 2014. Fossil Kajanthus juncaliensis gen. et sp . nov from Portugal: Floral bear witness for Early Cretaceous Lardizabalaceae (Ranunculales, basal eudicot). Grana 53:283–301.
Rothwell GW, Crepet WL, Stockey RA. 2009. Is the anthophyte hypothesis live together with well? New bear witness from the reproductive structures of Bennettitales. American Journal of Botany 96:296–322.
Rothwell GW, Stockey RA. 2016. Phylogenetic diversification of Early Cretaceous seed plants: The chemical compound seed cone of Doylea tetrahedrasperma. American Journal of Botany 103:923–937.
Schlee M, Göker M, Grimm GW, Hemleben V. 2011. Genetic patterns inwards the Lathyrus pannonicus complex (Fabaceae) reverberate ecological differentiation rather than biogeography together with traditional subspecific division. Botanical Journal of the Linnéan Society 165:402-421.
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