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Research paper
Rhododendron kuomeianum (Ericaceae), a new species from
northeastern Yunnan (China), based on morphological and genomic
data
Yu-Hang Chang
a
,
b
,
1
, Gang Yao
a
,
b
,
1
, Jens Neilsen
c
, De-Tuan Liu
a
,
b
, Lu Zhang
d
,
Yong-Peng Ma
a
,
b
,
*
a
Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences,
Kunming, Yunnan 650201, China
b
Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
c
Dobbies Garden Centre, UK-DD2 Perth, Scotland, UK
d
Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan 650051, China
article info
Article history:
Received 28 September 2020
Received in revised form
7 April 2021
Accepted 13 April 2021
Available online xxx
Keywords:
Rhododendron
New species
RAD-seq
Phylogenetic position
abstract
Rhododendron kuomeianum Y.H. Chang, J. Nielsen &Y.P. Ma, a new species of Rhododendron (Ericaceae)
within subsect. Maddenia in sect. Rhododendron from Yiliang County, NE Yunnan, China, is described and
illustrated. The new species is similar to R. valentinianum, but it can be easily distinguished by its sparse
scales on the abaxial surface of the leaf blade, fewer flowers per inflorescence and white corolla with pale
red margins. There are also differences in the widths of calyx lobes, leaf blade shape and indumentum
characteristics of the petiole between the new species and Rhododendron linearilobum. We confirmed
that R. kuomeianum is a new species closely related to R. valentinianum and R. changii with phylogenomic
studies of 10 species within this subsection based on restriction site-associated DNA sequencing (RAD-
seq) data. These phylogenomic analyses also clarified additional taxonomic problems in this subsection
previously raised by morphological analysis. Our findings make a strong case for using next-generation
sequencing to explore phylogenetic relationships and identify new species, especially in plants groups
with complicated taxonomic problems.
Copyright ©2021 Kunming Institute of Botany, Chinese Academy of Sciences. Publishing services by
Elsevier B.V. on behalf of KeAi Communications Co. Ltd. This is an open access article under the CC BY-
NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
1. Introduction
Rhododendron L. is the largest genus in Ericaceae. It contains
about 1025 species and can be classified into eight subgenera (Fang
and Min, 1995;Chamberlain et al.,1996). Members of this genus are
distributed widely in the northern hemisphere, with the Sino-
Himalayan as the main center of abundance and diversity (Fang
and Min, 1995). Because of its high ornamental value and long
history of cultivation, rhododendrons have become popular horti-
cultural plants worldwide. Rhododendron species richness is high-
est in China, which also contains numerous endemic species (Fang
et al., 2005). In fact, an estimated 600 Rhododendron species have
been described in China, and large numbers of new taxa are still
being discovered since the publication of Flora of China (Gao and
Zhang, 2008;Gao and Li, 2009;Chen et al., 2010,2012;Ma et al.,
2013,2015;Liao et al., 2015;Cai et al., 2016;Liu et al., 2018;Tian
et al., 2019).
In recent years, field investigations in Yiliang County (Zhaotong
prefecture), within the Wumeng Mountain system in northeastern
Yunnan, China, have discovered several new species of Rhododen-
dron (Gao and Zhang, 2008;Gao and Li, 2009;Tian et al., 2019),
suggesting that Rhododendron diversity in this region has been
*Corresponding author. Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of
Sciences, Kunming, Yunnan 650201, China.
E-mail address: mayongpeng@mail.kib.ac.cn (Y.-P. Ma).
Peer review under responsibility of Editorial Office of Plant Diversity.
1
These authors contributed equally to this work.
Contents lists available at ScienceDirect
Plant Diversity
journal homepage: http://www.keaipublishing.com/en/journals/plant-diversity/
http://journal.kib.ac.cn
https://doi.org/10.1016/j.pld.2021.04.003
2468-2659/Copyright ©2021 Kunming Institute of Botany, Chinese Academy of Sciences. Publishing services by Elsevier B.V. on behalf of KeAi Communications Co. Ltd. This
is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Plant Diversity xxx (xxxx) xxx
Please cite this article as: Y.-H. Chang, G. Yao, J. Neilsen et al.,Rhododendron kuomeianum (Ericaceae), a new species from northeastern Yunnan
(China), based on morphological and genomic data, Plant Diversity, https://doi.org/10.1016/j.pld.2021.04.003
underestimated. During field investigations in this region in June
2018, we collected specimens from a Rhododendron population
with white flowers that were growing on steep cliffs and rocks.
After a detailed examination of relevant specimens and litera-
ture, we concluded that these specimens represent a species
new to science in subsect. Maddenia (Hutch.) Sleumer in subgen.
Rhododendron.
Morphologically, this species is similar to Rhododendron valen-
tinianum Forrest ex Hutch. and Rhododendron changii (W. P. Fang)
W. P. Fang: it has a broadly elliptic to obovate leaf blade, rusty-
yellow setae on the petiole and funnelform-campanulate corollas.
However, the new species can be distinguished from these species
by having sparse scales on the abaxial surface of the leaf blade, 1e2
flowers per inflorescence, and a larger, white corolla. Although both
the new species and Rhododendron linearilobum R. C. Fang &A. L.
Chang have similar corollas, the new species can be distinguished
by having a broadly elliptic to obovate leaf blade, dense rusty-
yellow setae on the petioles, and wider calyx lobes.
In recent years, as many new species have been described,
molecular marker technology has greatly advanced our under-
standing of Rhododendron phylogeny (Gao et al., 2003;Ma et al.,
2013;Yan et al., 2014;Liu et al., 2018;Du et al., 2020). However,
these studies have mainly relied on a few common markers, which
have limited their resolution. Next Generation Sequencing (NGS)
offers a solution to these issues (Hohenlohe et al., 2010). For
example, restriction site-associated DNA sequencing (RAD-seq) has
been widely used in non-model species (e.g., temperate bamboos)
to resolve evolutionary relationships (Heckenhauer et al., 2018;
Zhang et al., 2018;Liu et al., 2020;Guo et al., 2020).
Here we confirmed that our newly collected specimen is a
hitherto undescribed species using RAD-seq data to reconstruct the
phylogenetic relationships of 11 Rhododendron species.
2. Materials and methods
2.1. Morphological analysis
During field investigations in June 2018 in Xiaocaoba Nature
Reserve, Zhaotong prefecture, northeastern Yunnan, China, speci-
mens of the new species were collected. Some living plants were
introduced and cultivated at the Kunming Botanical Garden,
Kunming Institute of Botany, CAS. The microscopic morphology of
leaves was observed through a KEYENCE VHX-6000 stereoscopic
microscope (KEYENCE Corp., Osaka, Japan). In addition, three
similar species were sampled for morphological comparison. All
voucher specimens in this study were deposited in the herbarium
of the Kunming Institute of Botany (KUN), CAS.
2.2. Restriction site-associated DNA sequencing and SNP
identification
A total of 11 individuals were sampled to construct the phylo-
gram (Appendix A). Because the morphological characters of the
new species are very similar to species within subsect. Maddenia in
Rhododendron, we sampled nine additional species within the
subsection and selected Rhododendron simsii Planch. as the out-
group for subsequent phylogenetic analysis. High quality genomic
DNA was extracted from silica gel dried young leaves using a
modified CTAB protocol (Doyle, 1991).
The RAD-seq library was prepared using EcoRI to digest DNA,
following the adapted protocol of Miller et al. (2007). The de novo
assembly of the RAD-seq library and SNP genotyping from short-
read sequences was performed using the STACKS 2.5.2 pipeline
(Rochette, 2017,2019). The raw data was demultiplexed and filtered
using the process_radtags program (key parameters included -c -q
-E -t 135). For each sample, short-reads were merged into loci
based on a maximum likelihood framework using the program
ustacks, and were then aligned into exactly-matching stacks. The
stackedepth parameter was set to three (m ¼3) and the within-
individual distance parameter was five (M ¼5). The catalog of
loci from all samples was built using cstacks with a between-
individual distance parameter of three (n ¼3). Lastly, the loci of
each sample were matched against the catalog to confirm alleles
via the program sstacks. To reconstruct a phylogenetic tree, we
randomly selected one SNP from each locus via the program pop-
ulations. The SNP obtained from the previous STACKS pipeline was
first applied by VCFtools (Danecek, 2011) with the following key
parameters: –min-alleles 2 –max-alleles 2 –remove-indels –maf
0.05 –max-missing 0.2, –minGQ 30 –minDP 3.
After filtering with VCFtools, 42,083 SNPs were obtained and
then tested for neutrality using the key parameter Tajima's D with
the sliding windows of 2500 and a 95% confidence interval (Tajima,
1989). The VCF file of neutral site was converted to phy format
using Tassel 5.0 (Bradbury et al., 2007). Phylogenetic analysis of SNP
matrices in phy format was performed using the maximum likeli-
hood method of concatenation using IQTREE (Minh et al., 2020;
Kalyaanamoorthy et al., 2017;Hoang et al., 2018) on partition A of
the Beijing Supercloud Computing Center, and the best base sub-
stitution model selected from 242 DNA base substitution models
was TVMþFþASC, and the bootstrap was set as 1000. Phylogenetic
trees were graphically visualized using FigTree (Price et al., 2010).
To capitalize on phylogenetic information from the sequencing
data and obtain a robust taxonomic status for the new species, SNP
loci were genotyped based on the de novo assembly of the RAD-seq
data. After non-linkage filtering and neutral tests, we genotyped 12,
380 loci. By calculating and sorting the BIC scores for these geno-
typed sites, the TVMeþASC model was selected as the best-fit
model for the maximum likelihood method of the phylogenetic
tree.
3. Results
3.1. Morphological characters
The morphological characters of the new species differ from all
species previously described in Rhododendron. Several traits of the
new species indicate that it belongs to the subsect. Maddenia;
specifically, it has a large corolla, the abaxial surface of the leaf is
scaly, and a quarter of the base of the style has scales (Figs. 1 and 2).
The new species can be distinguished from the two most similar
species (i.e., R. valentinianum and R. changii) by having sparse scales
(ca. 1e2their own diameter apart) on the abaxial surface of leaf
blade (Fig. 3), fewer flowers (1e2) per inflorescence, and a larger,
white corolla (3.5e4.5 cm) (Table 1). R. linearilobum has a corolla
with similar morphology and color as the new species, but can be
easily distinguished from the new species by having a narrowly
obovate leaf blade, densely rusty-red-villous petiole, and calyx
lobes ca. 2 mm in width (Table 1).
3.2. Data generation and molecular phylogeny
We constructed a RAD-seq libraries and genotyped SNPs from
11 species of Rhododendron. A total of 4.6 gigabase pairs (gb) of
data was obtained, with an average of 428.22 megabase pairs (Mb)
of data per sample (see Appendix B for details).
Phylogenetic trees based on the de novo assembly of our RAD-
seq library reveal that all 10 species within subsect. Maddenia are
clustered into one clade, with Rhododendron maddendii subsp.
crassum (Franchet) Cullen as the basal species (Fig. 4). One subclade
includes R. valentinianum,R. changii,Rhododendron pachypodum
Y.-H. Chang, G. Yao, J. Neilsen et al. Plant Diversity xxx (xxxx) xxx
2
Balf. f. &W. W. Smith and Rhododendron kuomeianum Y.H. Chang, J.
Nielsen &Y.P. Ma sp. nov., which verifies that R. kuomeianum is
genetically distinct and supports its status as a new species.
Notably, the topological structure of the ML tree indicates that the
phylogenetic position of R. valentinianum is very close to that of
R. changii. The remaining five species (Rhododendron liliiflorum
Levl., Rhododendron chunienii Chun &Fang, Rhododendron maddenii
subsp. maddenii (Batalin) H. Hara, Rhododendron excellens Hemsl. &
Wils. and Rhododendron ciliatum Hook. f.) cluster into a separate
subclade, although R. liliiflorum and R. chunienii cannot be distin-
guished from each other. In addition, R. maddenii subsp. maddenii is
genetically distant from the subspecies R. maddenii subsp. crissum
(Fig. 4).
4. Discussion
In the present study, morphological comparisons and phyloge-
netic analysis based on de novo assembly of a RAD-seq library
confirmed that R. kuomeianum is a new species. R. kuomeianum has
similar floral traits as R. linearilobum; however, the new species has
an oblong-elliptic leaf blade similar to R. valentinianum and R. changii.
Due to unavailability of sequencing materials of R. linearilobum,
which was estimated to be <50 plants and hence evaluated to be
critically endangered by IUCN criteria (Gibbs et al., 2011), the most
genetically close relative remains to be unclear.
Rhododendron is the largest genus of seed plants in China, and
recognized as one of the most taxonomically challenging plants due
to recent adaptive radiations and natural hybridization (Yan et al.,
2014). One major taxonomic problem for this genus is that many
hybrids have been incorrectly identified as new taxa. Previous
Fig. 1. Illustrations of Rhododendron kuomeianum Y.H. Chang, J. Nielsen &Y.P. Ma sp.
nov. Drawn by R.M. Zhang. (A) habit; (B) corolla; (C) dissected corolla; (D) inflorescence
bud; (E) flower bud; (F) stamen; (G) pistil and calyx; (H) leaf adaxial surface; (I) leaf
abaxial surface; (J) distribution of scales on the adaxial surface of the leaf blade; (K)
single scale on the abaxial surface of leaf blade; (L) capsule.
Fig. 2. Rhododendron kuomeianum Y.H. Chang, J. Nielsen &Y.P. M a sp. nov. (AeB) plant and habitat; (CeD) leaf; (E) inflorescence bud; (F) corolla anatomy; (G) fruit. Scale bar ¼1 cm.
Y.-H. Chang, G. Yao, J. Neilsen et al. Plant Diversity xxx (xxxx) xxx
3
studies at the Baili Rhododendron Nature Reserve in Guizhou have
confirmed that many of the new taxa described in this area are
actually different genotypes produced by natural hybridization
between Rhododendron delavayi Franch. and Rhododendron irror-
atum Franch (Marczewski et al., 2016;Zhang et al., 2017).
Morphological evidence has been used to describe taxa for over a
century; however, this approach often leads to uncertainty and
debate. For instance, R. changii was initially described as a variety of
R. valentinianum; subsequently, it was upgraded to species status
because of its larger, scaleless corolla, glabrous style, and the
absence of hairs on the pedicel or calyx (Fang, 1983). After
comparing holotypes and native plants, Geng (2014) restored
R. changii as a variety of R. valentinianum based on morphological
similarities and habitats. Our phylogenetic tree clusters these
two species together, indicating that R. changii can reasonably
be treated as a variety of R. valentinianum. Similarly, Li (1995) and
Geng (2004) proposed that the holotype of R. chunienii, which
had previously been described as having five stamens (the most
unique character in this subsection), had been misdiagnosed
because of damage to the corolla. Both living plants and specimens
of R. chunienii collected at the type locality have 10 stamens;
furthermore, other characteristics of R. chunienii are the same as in
R. liliiflorum. Thus, R. chunienii has been treated as a synonym for
R. liliiflorum. Our phylogenetic analysis supports this classification.
Rhododendron maddenii contains two subspecies, R. maddenii
subsp. maddenii and R. maddenii subsp. crassum. Although these
subspecies are morphologically similar, they are geographically
isolated from one another. R. maddenii subsp. maddenii is mainly
distributed in Cuona County and Naidong District in southern Tibet,
China, as well as in Bhutan and northeastern India; in contrast,
R. maddenii subsp. crassum is mainly distributed in western
Yunnan. In this study, the high-confidence phylogenetic tree
Fig. 3. The micrograph of the leaf surface of Rhododendron kuomeianum Y.H. Chang, J. Nielsen &Y.P. M a sp. nov. (A) distribution of scales on the adaxial surface of the leaf blade; (B)
distribution of scales on the abaxial surface of leaf blade; (C) single scale on the on the adaxial surface of the leaf blade; (D) single scale on the on the abaxial surface of leaf blade; (E)
indumentum characteristics of the petiole.
Table 1
Main morphological comparisons of Rhododendron kuomeianum with similar Rhododendron species.
Characters R. kuomeianum R. valentinianum R. changii R.linearilobum
Geographic distribution NE Yunnan SE W Yunnan
NW NE Guizhou
Chongqing SE Yunnan
Elevation 1800e2000 m 2400e3000 m 1600e2000 m 2200 m
Petiole setose setose setose villous
Shape of the leaf blade broadly elliptic to obovate obovate to oblong-elliptic obovate to oblong-elliptic elliptic
Size of leaf blade 3.5e5.5 2.5e3.5 cm 3e41.5e2cm 3e4.5 2e2.5 cm 4e7.5 1.5e2.5 cm
Scale density (as own diameter
apart)
1e2 0.5 or contiguous nearly contiguous 1e2
Inflorescence 1 or 2-flowered 2e4-flowered 3 or 4-flowered 2e4-flowered
Pedicel glabrous setose glabrous pubescent
Calyx lobes 4e73e5 mm, ovate or
broadly elliptic
84e5 mm, ovoid or oblong-
ovate
10 4e5 mm, ovoid or oblong-
ovate
6e12 2 mm, linear
Color of the corolla white with pale red margins light to bright yellow light to bright yellow white with pale red margins
Corolla size 3.5e4.5 cm long, tube 2e3cm
long
2e3.5 cm long, tube 1.8e2cm
long
3.5e4 cm long, tube 1.8e2cm
long
ca. 4 cm long, tube 1.8e2cm
long
Proportion of scales to style 1/4 1/8 1/8 2/5
Indumentum characteristics of
the style
glabrous glabrous glabrous base pubescent
Y.-H. Chang, G. Yao, J. Neilsen et al. Plant Diversity xxx (xxxx) xxx
4
reveals that the genetic difference between these two subspecies is
very large, which has also been confirmed by DNA barcoding (Ya n
et al., 2014). One explanation for the genetic differences between
these two subspecies is that long-term geographic isolation has
allowed mutations to accumulate in their respective populations.
4.1. Taxonomic treatment
4.1.1. Rhododendron kuomeianum Y.H. Chang, J.Nielsen &Y.P. Ma
sp. nov (Figs. 1 and 2)
国楣杜鹃.
4.1.1.1. Type. CHINA. Yunnan: Yiliang County Xiaocaoba Nature
Reserve, 25
50
0
01
00
N, 104
17
0
41
00
E, alt. 2000 m, 15 Apr. 2019, Y.H.
Chang,Y.P. Ma &D.T. Liu, Cyh20190402 (holotype KUN! 1498888;
isotype KUN! 1498889, 1498890).
4.1.1.2. Diagnosis. Rhododendron kuomeianum resembles
R. valentinianum in having a broadly elliptic to obovate leaf
blade, dense rusty-yellow setae on the petiole, and a funnelform-
campanulate corolla. It differs from R. valentinianum in having a
white corolla with a pale red margin (versus light to bright yellow),
fewer flowers (1e2) per inflorescence (versus 2e4), and sparser
distribution of scales on the abaxial surface of the leaf blade
(1e2scales diameter apart) (versus 0.5 scales diameter apart)
(Table 1).
4.1.1.3. Description. Multi-branched shrubs, evergreen, 40e10 0 cm
tall; branches short, old branches deep red to brown, young shoots
scaly, hispid. Petiole 5e9 mm, scaly, hispid; leaf blade leathery,
broadly elliptic to obovate, 3.5e5.5 2.5e3.5 cm; base broadly
cuneate or rounded; margin entire and slightly revolute, sparsely
setose; apex obtuse or rounded, apiculate; abaxial surface pale
green, scales 1e2their own diameter apart, about equal in size,
golden, seldom contiguous, adaxial surface deep green and shiny,
densely scaly, brown hispid along midrib; midveins raised adax-
ially and lateral veins hardly raised; midrib concave adaxially.
Inflorescence terminal, cymose, 1 or 2-flowered. Pedicel stout,
0.6e0.9 cm, scaly, without hairs; calyx 4e5-lobed to the half, lobes
pale green, 4e73e5 mm, ovate or broadly elliptic, persistent in
fruit, scaly abaxially and on margin, margin sparsely white-ciliate;
corolla funnelform-campanulate, white with pale red margin and
without blotch, 3.5e4.5 cm, tube 2e3 cm, outer surface glabrous,
lobes orbicular or broadly elliptic, ca. 1.8e2.5 2.0e2.5 cm; sta-
mens 10, 1.5e3.7 cm, unequal, shorter than corolla; filaments
densely pubescent in lower 1/5; anthers oblong-elliptic, red
brown, ca. 2.5e3 mm; ovary 5-locular, ca. 4.5 mm, densely scaly;
style slightly arched, as long as corolla or exserted from corolla,
3.5e4.2 cm base densely sca ly in lower 1/4. Capsule ovoid, c a. 1 cm,
dehiscing from top, densely scaly. Flowering: AprileMay, Fruiting:
after June.
4.1.1.4. Paratype. China. Yunnan: Yiliang county Xiaocaoba Nature
Reserve, 25
50
0
06
00
N, 104
17
0
39
00
E, alt. 1950 m, 5 Apr. 2019, YH.
Chang &F.M. Yang, Cyh20190401 (KUN! 1498891). Same locality,
alt. 2030 m, 6 June 2018, Y.P. Ma,Y.H. Chang &J. Neilsen,
Ma20180603 (KUN! 1498892, 1498893).
Fig. 4. Maximum likelihood phylogenetic topology based on 12380 unlinked high-quality and neutral SNP sites without a reference genome. The phylogenetic tree bootstrap
probabilities 75 are shown at branches.
Y.-H. Chang, G. Yao, J. Neilsen et al. Plant Diversity xxx (xxxx) xxx
5
4.1.1.5. Distribution and habitat. To date, Rhododendron kuomeia-
num has only been found in the type locality at Xiaocaoba Nature
Reserve, Zhaotong City, NE Yunnan, China, where it is represented
by one population at elevations of 1800e2000 m (Fig. 5). In addi-
tion, we found all plants growing on rocks and cliffs, which are
steep and barren (Fig. 2A). Based on the known occurrences, we
conclude that R. kuomeianum is well-adapted to cold and wet
environments.
4.1.1.6. Conservation status. During many field investigations since
2018, we have only found this species in the type locality, and there
are about 200 mature individuals in this population. Detailed ex-
amination of relevant specimens and literature available for
Rhododendron species collected from Xiaocaoba Nature Reserve
and adjacent regions revealed no additional information about the
distribution of this species; therefore, this species is likely to be
endemic to this region. Based on the limited information currently
available, we thus tentativelyassign this species to an IUCN Red List
status of Data Deficient (DD) (IUCN, 2019). Further field investiga-
tion is urgently needed.
4.1.1.7. Etymology. The new species Rhododendron kuomeianum
was named after Professor Kuo Mei Feng, a botanist and horti-
culturalist from the Kunming Institute of Botany, Chinese Academy
of Sciences, to honor his great contribution to research on the genus
Rhododendron in China. In pinyin, the Chinese name is “Gu
om
ei dù
ju
an”.
Author contributions
Y.P. Ma conceived and designed experiments. Y.H. Chang, Y.P.
Ma, D.T. Liu, and J. Neilsen performed field investigations and
collected the specimens. G. Yao and L. Zhang analyzed the molec-
ular data. Y.H. Chang wrote the manuscript. Y.H. Chang, G. Yao and
Y.P. Ma revised the manuscript.
Declaration of competing interest
We declare that the named authors have no conflicts of interest,
financial or otherwise.
Acknowledgments
We are grateful to Mrs. Rongmei Zhang for the botanical line
drawing, Mr. Lianyi Li for the microscopic scanning of the leaf
surface, Ms. Songting Du, Mrs. Wei Wei, and Mr. Yechun Xu for
providing photos and Mr. Fengmao Yang for help during fieldwork.
We also thank Mr. Shiwei Guo for his constructive comments on the
manuscript. This study was financially supported by the National
Natural Science Foundation of China (Grant No. 31770418 and No.
31760231) the Youth Innovation Promotion Association, Chinese
Academy of Sciences (Grant No. 2018428), and the Reserve Talents
for Academic and Technical Leaders of Middle-aged and Young
People in Yunnan Province (Grant No. 2018HB066).
Appendix A and B. Supplementary data
Supplementary data to this article can be found online at
https://doi.org/10.1016/j.pld.2021.04.003.
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