Background—What nosotros know virtually Zelkova
Zelkova is a minor Ulmaceae (elms too relatives) genus amongst v or half-dozen species that demo a disjunct distribution pattern: inward western Eurasia, nosotros withdraw maintain the geographically really restricted species Z. sicula on Sicily, Z. abelicea on Crete, too Z. carpinifolia inward scattered inward Georgia (Transcaucasia) to northern Iran. In East Asia, nosotros withdraw maintain i or 2 species that survived only inward Red People's Republic of China proper (Z. schneideriana too Z. sinica), too i widespread species inward China, the Korean peninsula, too Japan: Z. serrata. The biogeographic blueprint of the genus appears to live trivial: the western Eurasian too East Asian species each shape a lineage. In the western Eurasian lineage, the Mediterranean species Z. abelicea too Z. sicula are unopen sisters (Denk & Grimm 2005; Christe et al. 2014). In the East Asian lineage, molecular information so far failed to separate Z. schneideriana (and Z. sinica, if the lean information are genuine) from the widespread Z. serrata. However, ITS patterns shared betwixt Z. carpinifolia and the East Asian species Z. serrata, are indicative for a recent split, or a longer contact betwixt Z. carpinifolia and Z. serrata. This may withdraw maintain left a persisting imprint inward the biparentally inherited nuclear cistron regions (such as ITS) but cannot live captured past times the maternally inherited plastomes, primarily sorted past times geography. But whereas the genetic differentiation inward the western Eurasian species is good studied (Christe et al. 2014), the information for Eastern Asia are soundless scarce. Being non feasible, neither nosotros (Denk & Grimm 2005) nor Christe et al. provided an explicit biogeographic-historical reconstruction, a so-called ‘ancestral expanse analysis’ (AAR). Where the newspaper of Zhang et al. aimed to step-in.Zhang et al.'s study—according to their abstract
Zhang et al. “… sequenced too combined ITS too trnL-trnF, psbA-trnH [correct order: trnH-psbA], and rbcL to reconstruct a phylogenetic tree.” Using Bayesian dating, “the historic menstruum of Zelkova was traced to Cretaceous ca. lxx Ma, the crown departure historic menstruum of the Ulmaceae. Generic diversification was started at Paleocene ca. 53 Ma.” Not a result, but an assumption: the respective node heights, ages, were accordingly constrained. They applied several AAR methods: “Based on the reconstructed ancestral area, northeastern Red People's Republic of China was speculated to live the house of origin, from where species migrated westward to western Asia–southern Europe too dispersed to Nippon too Korea inside East Asia.” too farther “presumed” that “the Chinese subtropical region” [i.e. today the due south of China] is the “diversity center” [trivial: the only part amongst 3 species; however, the AARs only scored for “China” too “China + Japan”], too that the genus’ distribution blueprint relates to the “East Asian monsoon onslaught at virtually 22 Ma as good as the Qinghai–Tibetan Plateau uplift” [always a skilful guess]. The lastly judgement of the abstract states that: “Species extinction inward northeastern Red People's Republic of China perhaps coupled amongst the climate cooling event, the glacial epoch during the Quaternary.” Let lone the somewhat awkward phrasing (the native English-speaking co-author died vii months before the newspaper was submitted), everything stated inward the abstract or conclusions that is non trivial, is without whatsoever basis.Zhang et al.’s prime number error: wretched information basis
No georeferenced samples…
Fig. 1 inward Zhang et al. shows a distribution map of Zelkova species, but none of these points were genuinely sampled past times the authors. Instead they sequenced the iv said cistron regions for 12 individuals, including nine from botanical gardens (one only sequenced for rbcL): the 2 Z. carpinifolia, the Georgian-Iranian species, too the residue representing the East Asian species Z. serrata, Z. sinica (possibly a mis-determination), too Z. schneideriana growing inward Red People's Republic of China inward the wild (Z. sinica may indeed live extinct). The remaining 3 were from herbarium material: i Z. serrata from Sichuan (W. China), too each i of the 2 remaining western Eurasian species.Relying solely or by too large on arboretum cloth is problematic for 2 reasons:
- Being on tillage for mayhap to a greater extent than than i generation, arboretum trees may live (unnatural) hybrids.
- The provenance of the master copy seed/seedling maybe unknown.
… too probable unsuitable laid of markers
The authors combined the nuclear ITS part amongst 3 plastid regions, 2 non-coding spacers (trnL-trnF, slow-evolving; trnH-psbA, fast-evolving) too a highly conserved gene, the rbcL gene. Signal inward the ITS is nonetheless complex, too i has to bargain amongst intraindividual variation (Denk & Grimm 2005). The patterns constitute past times Christe et al. (2014) betoken a principal correlation betwixt ITS departure too combined trnL/trnH-psbA haplotypes (above species level), but they also relied on our ITS information for the East Asian species pointing to non-trivial differentiation patterns too a closer human relationship betwixt Z. carpinifolia and Z. serrata than seen inward plastid geneaologies.Zhang et al. write inward the showtime judgement of the results: “Bayesian inference of the ITS dataset too cpDNA datasets showed no [in]congruence [a mistyper; meet mail past times the authors from 1/9/2017] at top dog topological nodes of 2 phylogenetic trees [possible translation: no (highly) supported conflict betwixt ITS too cpDNA inferences]; thus, both datasets tin live combined into one.” Naturally, no documentation/proof is provided for this claim. The supplement EPS-files (a Bayesian inference too ML bootstrap cladogram) demo unambiguous back upward for the genera too the long-resolved relationships inside Zelkova (e.g. our report or Christe et al. 2014), but non so inward the East Asian lineage critical to the conclusions of the report (Fig. 1); which may live due to incongruence betwixt ITS too plastid data.
 |
| Fig. 1 The East Asian subtree of Zelkova, extracted from the Bayesian bulk dominion consensus tree (left) too ML tree (right) provided inward the "complimentary cloth fig. S1 too fig. S2" of Zhang et al. Note the depression posterior probabilites (PP, branch labels, left) for iv out of half-dozen (potential) branches, which tin live lower than ML bootstrap back upward (branch labels, right); a straight indication of problematic signal. The seat of "Z. serrata 5" may live a missing information artefact (rbcL likely invariable inside this lineage). No phylograms are provided, the information are soundless confidential, so the actual branch-lengths are unknown. |
The trnL-trnF spacer too rbcL gene regions are low-divergent to invariable too ofttimes uninformative below the genus aeroplane inward many northern-hemispheric extratropical tree genera. In fact, branches amongst lower Bayesian PP than ML BS back upward inward the East Asian subtree of Zhang et al. may live an indication for a lack of discriminating signal inward all combined cistron regions.
[Zhang et al. withdraw maintain so far non released or shared their data, the provided GenBank accession numbers are soundless confidential too a information matrix has non been provided. Once their information are released, I’ll render a total re-investigation of all available information on the genus.]
Zhang et al.’s minute major error: bad root
H5N1 chronogram, a dated tree, is a rooted ultrametric phylogenetic tree. Thus, its historic menstruum estimates depend on a well-informed root too reasonably estimated branch-lengths. Zhang et al. included also Ulmus (5) too Hemiptelea (2 samples) of the Ulmaceae, too Celtis (1) too Pteroceltis (2) of i of their sis families, the Cannabaceae. As node constraints, they relied on an obscure, partly misinterpreted mix of secondary evidence (ages estimated past times others) to constrain the minimum root historic menstruum of their tree to lxx Ma. They considered lxx Ma a valid estimated for the “crown historic menstruum of Ulmaceae”, i.e. the minimum historic menstruum of the ‘most recent mutual ancestor’ (MRCA) of Hemiptelea, Ulmus and Zelkova. In addition, they fixed the stalk (root) ages (probably, their description on p. 4 is a fleck confused) of Ulmus and the East Asian Zelkova lineage to fifty Ma based on “early fossil[s] constitute inward northeastern China” (p. 4). Unfortunately, they forgot to properly root their tree before the dating. In their tree, Zelkova is sis to the remaining Ulmaceae, which shape a grade, too the Cannabaceae are placed as sis to Hemiptelea (possibly long branch attraction). And as lawsuit the constrained nodes are closer to the tree root than they should live (Fig. 2); too the lxx Ma are used for the MRCA of Ulmaceae and Cannabaceae, non only Ulmaceae.
Age estimates using relaxed or strict clock models are farther the production of branch-lengths (relative or absolute), which brings us dorsum to the information basis: the combined regions demo probable dissimilar departure levels, too this is especially problematic when comparison ingroup variety (Zelkova) amongst the variety betwixt genera (Ulmus, Hemiptelea) too families (Ulmaceae vs. Cannabaceae).
Zhang et al.’s concluding nails inward the coffin:
Poor ancestral expanse coding …
The thought of the report was to scope an AAR (ancestral expanse reconstruction) for the genus. The authors hypothesise a north-eastern Chinese source of the genus. For the geographically highly restricted western Eurasian species geographic scoring is trivial: the Mediterranean sis species Z. abelicea (Crete) too Z. sicula (Sicily) were scored as “southern Europe (D)” (labelled “North America” [?!] inward their fig. 3), too the Transcaucasian-Iranian Z. carpinifolia as “West Asia (C)” (labelled “Europe”[!] inward their fig. 3). Zhang et al. scored their Z. sinica too Z. schneideriana as “China (A)”; both species are – according to their ain tree – a subset of the widespread Z. serrata, all of which were scored as “China + Nippon (and Korea) (AB)” lacking proper provenance information. Meaningful would withdraw maintain been, regarding the authors’ hypothesis, to score only southern, southwestern (subtropical) Chinese cloth as ‘A’, too north-eastern Chinese-Korean-Japanese cloth as ‘B’. The authors speculate too verbalize over that the genus originated inward north-eastern China, which is closer to Korea too as distant from Nippon as it is from the southern too southwestern Zelkova populations inward China. Biogeographic scoring should live done adapted to the top dog inquiry of a study, too non based on political boundaries (or other artificial standards).OTUs (‘operational taxonomic units’; tip taxa) should also non live scored as ambiguous. If a species is constitute inward 2 (or more) of the used biogeographic regions, i needs cloth from each region. If only cloth from i part is available, only that part must live scored. For Zhang et al., a meaningful coding was in all likelihood impossible due to the lack of georeferenced cloth of Z. serrata. Thus, they lacked precisely the cloth crucial for what they wanted to study.
… too mis-interpretation of AAR results
Using 2 tools amongst dissimilar AAR algorithms Zhang et al. (p. 5) found: “The ancestral expanse of Zelkova inward S-DIVA [method 1] was shown as air conditioning [=West Asia+China] or AD [geographically impossible], since H5N1 was the intersection of both areas air conditioning too AD; therefore, H5N1 [=China] may live elected as the ancestral expanse of Zelkova. Similarly, the DEC resultant [method 2] showed that the ancestral expanse of Zelkova was A, as the intersection of H5N1 too ABCD [= no idea].” Left aside the awkward phrasing, this is nonsense. Naïvely applied biogeographic inference methods ignoring the fossil tape are non only biased past times the current-day province of affairs (in Zhang et al.’s instance 8 of the 12 included OTUs where scored for solely or mayhap China), when their resultant is ambiguous so all results must live discussed or the analysis discarded as useless.The latter applies inward Zhang et al.'s case. One does non withdraw whatsoever sophisticated inference amongst ambiguous results to position frontwards the authors' hypothesis. Common feel would suffice. Just based on the current-day province of affairs (see also Fig. 2), i could hypothesise the genus originated inward Red People's Republic of China too migrated due west too north; although it may live non that easy, when nosotros include evidence from the fossil record, morphology, too ITS mutation pattersn (see give-and-take inward Denk & Grimm 2005).
Zhang et al.—A highly valuable bad example
The report of Zhang et al., too every bit bad studies, expose the inefficiency of the widely applied non-transparent (“confidential”) peer review system to forestall the publication of scientifically obscure too badly crafted papers (not rarely, but also non exclusively, the products of tireless Chinese researchers inward desperate withdraw of publications inward international peer-reviewed journals who squad upward amongst a retired, more-or-less accomplished USA scientist to increase their chances). Tree Genetics & Genomes is (well, was, its Impact Factor falters) a proper mid-tier mag amongst focus on population genetics; too I tin only speculate why the editor, Pär Ingvarsson, accepted (“communicated”) the paper (with honour to the decreasing Impact Factor, 2.4 inward 2014 to 1.6 inward 2016, i argue may live to larn a concur on the booming Chinese scientific discipline market).Aside from that, it’s a very fine representative of how non to scope a biogeographic inference. Errors done past times Zhang et al. tin live constitute inward many other flora biogeographic papers, but maybe non so piece of cake to see. Here, yous withdraw maintain them all together on 10 printed pages, which is a dainty service for academy teachers. You tin impress out the paper, manus it over to your (under)graduate or Ph.D. students too withdraw maintain them brand a list, what went incorrect here. And, if yous discovery the time, yous tin engage inward a give-and-take on the confidential peer review organization afterwards.
Linked material
My postReferences
Christe C, Kozlowski G, Frey D, Bétrisey S, Maharramova E, Garfi G, Pirintsos S, Naciri Y. 2014. Footprints of past times intensive diversification too structuring inward the genus Zelkova (Ulmaceae) inward south-western Eurasia. Journal of Biogeography 41:1081–1093.Denk T, Grimm GW. 2005. Phylogeny too biogeography of Zelkova (Ulmaceae sensu stricto) as inferred from leafage morphology, ITS sequence information too the fossil record. Botanical Journal of the Linnéan Society 147:129-157.
Zhang M-L, Wang L, Lei Y, Sanderson SC. 2017. Cenozoic evolutionary history of Zelkova (Ulmaceae), evidenced from ITS, trnL-trnF, psbA-trnH, and rbcL. Tree Genetics too Genomes 13:111 [e-paper]. https://link.springer.com/article/10.1007/s11295-017-1182-4; meet here for an annotated version.
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