Fuentes Bazan - Etal2012a Chenopodium Chenopodiac

Molecular Phylogenetics and Evolution 62 (2012) 359–374
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Molecular Phylogenetics and Evolution

journal homepage: www.elsevier.com/locate/ympev
Towards a species level tree of the globally diverse genus

Chenopodium (Chenopodiaceae)
Susy Fuentes-Bazan a,b, Guilhem Mansion a, Thomas Borsch a,⇑
a
Botanischer Garten und Botanisches Museum Berlin-Dahlem und Institut für Biologie, Freie Universität Berlin, Dahlem Centre of Plant Sciences,
Königin-Luise-Straße 6-8, 14195 Berlin, Germany
b
Herbario Nacional de Bolivia, Universidad Mayor de San Andrés (UMSA), La Paz, Bolivia
a r t i c l e i n f o a b s t r a c t
Article history: Chenopodium is a large and morphologically variable genus of annual and perennial herbs with an almost
Received 21 March 2011 global distribution. All subgenera and most sections of Chenopodium were sampled along with other gen-
Revised 28 September 2011 era of Chenopodieae, Atripliceae and Axyrideae across the subfamily Chenopodioideae (Chenopodiaceae),
Accepted 11 October 2011
totalling to 140 taxa. Using Maximum parsimony and Bayesian analyses of the non-coding trnL-F
Available online 24 October 2011
(cpDNA) and nuclear ITS regions, we provide a comprehensive picture of relationships of Chenopodium
sensu lato. The genus as broadly classified is highly paraphyletic within Chenopodioideae, consisting of
Keywords:
five major clades. Compared to previous studies, the tribe Dysphanieae with three genera Dysphania, Tel-
Chenopodium
Chenopodioideae
oxys and Suckleya (comprising the aromatic species of Chenopodium s.l.) is now shown to form one of the
Chenopodieae early branches in the tree of Chenopodioideae. We further recognize the tribe Spinacieae to include Spina-
TrnL-F cia, several species of Chenopodium, and the genera Monolepis and Scleroblitum. The Chenopodium rubrum
ITS and the Ch. murale-clades were newly discovered as distinct major lineages but their relationships within
Angiosperm phylogenetics Chenopodioideae will need further evaluation. Based on our results, we suggest the delimitation of Che-
Large genera nopodium to include Einadia and Rhagodia because these are part of the crown group composed of species
Polyploidy of subg. Chenopodium that appear sister to the Atripliceae. The tetraploid crops such as Ch. berlandieri
subsp. nuttalliae and Ch. quinoa also belong to Chenopodium sensu stricto. Trees derived from trnL-F
and ITS were incongruent within this shallow crown group clade. Possible biological causes are discussed,
including allopolyploidization.
Ó 2011 Elsevier Inc. All rights reserved.
1. Introduction tle’’]; Ch. pallidicaule Aellen [‘‘Cañihua’’]; and Ch. quinoa Willd. [‘‘Qui-
noa’’]) or weeds (Ch. ambrosioides L.; Ch. murale L.; Wiersema and
The genus Chenopodium sensu lato has been estimated to com- León, 1999). An integrative approach to a modern systematic treat-
prise some 150 species (Kühn, 1993). Most of them are annual herbs ment is therefore needed.
growing in arid or semi arid regions, and also on salt-rich soils. Com- Chenopodium belongs to the subfamily Chenopodioideae, within
pared to other plants of dry environments they lack typical adapta- the goosefoot family Chenopodiaceae (Caryophyllales). Chenopodi-
tions to such ecological conditions, such as the Kranz type leaf aceae contain approximately 100 genera and 1700 species, mainly
anatomy and the C4 photosynthetic pathway – both frequent in distributed in temperate and subtropical regions of both hemi-
other Chenopodiaceae (Carolin et al., 1975; Jacobs, 2001) – and suc- spheres (Aellen, 1960; Kühn, 1993; Welsh et al., 2003). Results of re-
culence. Morphologically, Chenopodium shows great variability in cent molecular phylogenetic analyses (e.g., Kadereit et al., 2003) are
leaf shape and indumentum, floral structures, inflorescence archi- in line with earlier classification systems with regard to this place-
tecture, and seed morphology (Aellen and Just, 1943; Kühn, 1993; ment of Chenopodium (see Kühn, 1993). Although phylogenetic rela-
Clemants and Mosyakin, 2003). While a large number of different tionships of major lineages within Chenopodiaceae still remain
species and intraspecific taxa have been described, the latest most poorly understood, the subfamily Chenopodioideae is considered
comprehensive synopsis dates back from around 60 years ago (Ael- to be monophyletic, based on sequence data of chloroplast rbcL
len and Just, 1943), despite the fact that several species are econom- (Kadereit et al., 2003) and matK/trnK (Müller and Borsch, 2005).
ically important either as crops (e.g., Chenopodium berlandieri Moq. While ongoing multigene analysis confirms the monophyly of
subsp. nuttalliae (Saff.) H.D. Wilson and Heiser, 1979 [‘‘Huauzon- the Chenopodioideae (Borsch et al., unpubl. data) all phylogenetic
studies hitherto carried out, indicate that Chenopodium is polyphy-
⇑ Corresponding author. Fax: +49 30 838 50218. letic. Species of Chenopodium were found in three different clades
E-mail address: t.borsch@bgbm.org (T. Borsch). within the Chenopodioideae. These clades were initially named
1055-7903/$ - see front matter Ó 2011 Elsevier Inc. All rights reserved.
doi:10.1016/j.ympev.2011.10.006
360 S. Fuentes-Bazan et al. / Molecular Phylogenetics and Evolution 62 (2012) 359–374
Chenopodieae I–III (Kadereit et al., 2003; Müller and Borsch, 2005) Understanding the origin and evolution of these crop plants as
and constitute the subfamily Chenopodioideae together with the of all other polyploids requires a species level phylogenetic frame-
tribe Atripliceae. Recent progress has been made in elucidating work of Chenopodium using organellar and nuclear genomic parti-
the evolutionary history of the Atripliceae based on DNA sequence tions in order to detect putative parental taxa. Currently there is no
data (Kadereit et al., 2010; Zacharias and Baldwin, 2010), in the phylogenetic framework at all for Chenopodium taking into account
context of which a distinct status of Axyrideae and Dysphanieae the extensive taxonomic, morphological, and biogeographic diver-
(both formerly Chenopodieae III) was also recognized. Neverthe- sity within the group. This study aims to clarify the phylogeny of
less, taxon sampling and tree resolution remain insufficient for a Chenopodium based on both cpDNA (trnL-F) and nrDNA (ITS), using
reliable circumscription of Chenopodium. The aromatic species extensive sampling within the genus and broad sampling across
are the only group of Chenopodium species that have been better other genera of Chenopodioideae, and also to examine whether
characterized phylogenetically. The first rbcL tree of Kadereit distinct subclades possess certain chromosome numbers as syna-
et al. (2003) revealed relationships between Dysphania glomulifera pomorphies and how ploidy levels are distributed in the group.
and other aromatic taxa within Chenopodieae III, but these lacked
statistical support. More recently Kadereit et al. (2010) included 2. Materials and methods
four aromatic species of Chenopodium along with Cycloloma,
Suckleya and Teloxys, providing greater confidence for a clade for 2.1. Taxon sampling
which the tribal name Dysphanieae was resurrected.
The complex taxonomic history of Chenopodium is summarized All three subgenera, and nine from 13 sections of Chenopodium
in Table 1, and shows over time large differences in the number sensu lato, were sampled, overall representing c. 50% of the spe-
of sections (between 2 and 13) and subsections that were cies. The sampling followed the most comprehensive treatments
recognized (Moquin-Tandon, 1849; Bentham and Hooker, 1880; of Aellen (1960), Table 2. Missing samples include only sect. Thel-
Ulbrich, 1934; Aellen and Just, 1943; Aellen, 1960; Scott, 1978a; lungia (1 sp. in Patagonia), sect. Polygnoidea (about 5 spp. in Austra-
Wilson, 1983; Mosyakin and Clemants, 1996; Judd and Ferguson, lia), sect. Tetrasepala (1 sp. in Australia) that clearly belongs to
1999; Clemants and Mosyakin, 2003). The most comprehensive Dysphania (Scott, 1978a), and sect. Auricoma that was covered by
treatments remain those of Aellen and Just (1943) and Aellen the rbcL analysis of Kadereit et al. (2003) and shows close affinity
(1960), upon which the morphology-based classification system to both Ch. desertorum and the Australian genera Einadia and
of Mosyakin and Clemants (1996, 2002) is largely based. Com- Rhagodia. The inclusion of the last two sections will therefore only
pared to the previous classification system, these authors recog- be relevant at species level within the respective subclades. We
nized the subg. Blitum within Chenopodium, and the distinct tried to represent species from various parts of the world within
genus Dysphania (Table 1). Mosyakin and Clemants (2002, 2008) these infrageneric entities, covering pronounced morphological
pointed out that Dysphania is the oldest name for this group differences between species as much as possible. Also, several indi-
and consequently re-classified the subgenus Ambrosia with all viduals from very widespread species (e.g., occurring on different
its sections under the generic name Dysphania. Although there continents) were sampled in order to get an idea if such morphol-
is now even increased phylogenetic support for the aromatic spe- ogy-based taxa correlate with molecular lineages.
cies to be a distinct group (Kadereit et al., 2010), the majority of We further sampled potentially close relatives of Chenopodium
aromatic species has never been included into any molecular within the Chenopodioideae: genera of the Chenopodieae I (Einadia
phylogenetic analysis. and Rhagodia; not included in Kadereit et al. (2003)), the Chen-
Chromosome counts in different species of Chenopodium show a opodieae II (Monolepis, Spinacia), the genus Suckleya (in Atripliceae
great extent of valences, from diploid (2n = 2x = 18) to hexaploid sensu Kühn, 1993; but in Dysphanieae according to Kadereit et al.,
(2n = 6x = 54; e.g. Aellen and Just, 1943; Uotila, 1973; Rahiminejad 2010), along with representatives of the tribes Atripliceae (Atriplex,
and Gornall, 2004; Bhargava et al., 2006). Based on these counts, a Grayia, Microgynoecium and Stutzia) and Axyrideae (Axyris, Cerato-
base number for Chenopodium of x = 9 was suggested (Aellen and carpus, Krascheninnikovia). Several taxa from Betoideae (Beta and
Just, 1943; Bhargava et al., 2006). However 2n = 2x = 16 chromo- Hablitzia) and Salsoloideae tribe Camphorosmeae (Bassia) (Table
somes were reported for Ch. ambrosioides (Uotila, 1973; Palomino 2) were used as outgroups based on the tree of Müller and Borsch
et al., 1990), while Spinacia oleracea was reported to deviate by (2005).
2n = 2x = 12 chromosomes (Ellis and Janick, 1960). Karyological
data were also not conclusive in improving the overall classifica- 2.2. DNA isolation, amplification and sequencing
tion of Chenopodium or in understanding relationships within the
Chenopodioideae. Genomic DNA was isolated from silica gel dried leaf tissue and
The degree of polyploidization encountered in Chenopodium herbarium specimens, using either a modified CTAB method
has been associated with hybridization processes (Rahiminejad (Borsch et al., 2003) or the Nucleo Spin Plant II extraction kit
and Gornall, 2004; Bhargava et al., 2006). Hybrid speciation has (Macherey Nagel, Düren, Germany). The quantity and quality of
been suggested to play an important role in Chenopodium, largely each DNA sample were measured by NanoDrop spectrophotometer
based on morphological observations, chromosome counts, (ND-1000, PeqLab, Erlangen, Germany).
hybridization experiments, allozyme and flavonoid analyses, The trnL-F region was amplified and sequenced using the forward
(Wilson, 1988; Wilson and Manhart, 1993; Uotila, 2001; Rahi- primer trnTAC2 (50 -CATTTTTCGGTATAGTAABCC-30 ), specifically de-
minejad and Gornall, 2004; Bhargava et al., 2006). The well- signed for the Amaranthaceae–Chenopodiaceae clade (this study)
known and economically important species Ch. quinoa and the standard reverse primer trnTf (50 -ATTTGAACTGGTGACAC
(2n = 4x = 36) and Ch. berlandieri subsp. nuttalliae (2n = 4x = 36) GAG-30 ; Taberlet et al., 1991). For some samples the standard
are both tetraploids of putative allopolyploid origin (Wilson and forward primer trnTc (50 -CGAAATCGGTAGACGCTACG-30 ; Taberlet
Manhart, 1993). Another case of morphologically allied species et al., 1991) was used for both amplification and sequencing. The
is the so-called Chenopodium album complex, members of which internal sequencing primers used were: trnL-460F (50 -GAGA
are reported as diploid, tetraploid or hexaploid but so far no hy- ATAAAGATAGAGTCC-30 ; Worberg et al., 2007) and trnTd
brid origin has been shown. For the origin of polyploidy in Cheno- (50 -GGGGATAGAGGGACTTGAAC-30 ; Taberlet et al., 1991). The ITS
podium album, endopolyploidy was reported and autopolyploidy region was amplified and sequenced with a specific Amarantha-
may also be involved (Kolano et al., 2008). ceae–Chenopodiaceae forward primer designed in this study:
Table 1
Historical overview on classification systems in Chenopodium L.
Moquin-Tandon (1849) Bentham and Hooker Ulbrich (1934) Aellen and Just (1943) Aellen (1960) Aellen (1978a) P.G. Wilson (1983) Mosyakin and Clemants (1996)
(1880)/ Volkens (1893)
Chenopodium L.
Subg. Ambrosia Subg. Ambrosida
Sect. Botryois Sect. Botrydium Sect. Botryoides Sect. Botryoides Sect. Botryoides Sect. Botryoides
Subsect. Botrys Subsect. Botrys (3) Subsect. Botrys
Subsect. Teloxys Subsect. Teloxys (3) Subsect. Teloxys
Sect. Ambrina Sect. Ambrina Sect. Ambrina Sect. Ambrina (4) Sect. Ambrina Sect. Ambrina
Sect. Orthosporum Sect. Orthosporum Sect. Orthosporum Sect. Orthosporum (4) Sect. Orthosporum Sect. Orthosporum
Subg. Blitum
Sect. Blitum Sect.Blitum
Sect. Pseudoblitum Sect. Pseudoblitum Sect. Pseudoblitum Sect. Pseudoblitum
S. Fuentes-Bazan et al. / Molecular Phylogenetics and Evolution 62 (2012) 359–374

Subsect. Viridia (4)
Subsect. Glauca (2)
Sect. Eublitum Sect. Eublitum Sect. Eublitum
Subsect. Capitata (2) Subsect. Capitata
Subsect. Foliosa (2) Subsect. Foliosa
Subg. Chenopodium Subg. Chenopodium Subg. Chenopodium
a
Sect. Agathophyton Sect. Agathophyton Sect. Agathophyton Sect. Agathophyton (2) Sect. Agathophyton
Sect. Degenia Sect. Degenia Sect. Degenia (1) Sect. Degenia Sect. Degeniaa
Sect. Desertorum (1)
Sect. Rhagodioides Sect. Rhagodioides Sect. Rhagodioides Sect. Rhagodiodes
Sect. Roubieva Sect. Roubieva Sect. Roubieva (1) Sect. Roubieva
Sect. Thellungia Sect. Thellungia Sect. Thellungia Sect. Thellungia
Sect. Skottsbergia Sect. Skottsbergia
Sect. Tetrasepala Sect. Tetrasepala
Sect. Auricoma Sect. Auricoma Sect. Auricoma
Sect. Chenopodiastrum Sect. Chenopodiastrum Sect. Euchenopodium Sect. Chenopodia Sect. Chenopodium Sect. Chenopodium Sect. Chenopodium Sect. Chenopodium
Subsect. Chenopodium Subsect. Chenopodium
Subsect. Glaucaa
Sect. Leprophyllum Sect. Leprophylum
Subsect. Undata Subsect. Undata (14) Subsect. Undata
Subsect. Leptophylla
Subsect. Urbica
Subsect. Fremontiana
Subsect. Favosa
Subsect. Standleyana
Subsect. Polysperma Subsect. Polysperma
Sect. Atriplicina
Sect. Margaritaria
Sect. Meiomeria
Subsect. Lejosperma Subsect. Lejosperma (43)
Subsect. Cellulata Subsect. Cellulata (21)
Ser. Foveasa
Ser. Cicatricosa Subsect. Cicraticosa
Subsect. Acuminata
Subsect. Grossefoveata (4) Sect. Grossefoveata
Sect. Polygonoidea Sect. Polygonoidea
a
Indicates sections which have been placed in different subgenera by the authors. Numbers in parentheses indicate the respective number of taxa sampled here with respect to the classification of Aellen (1960).
361
AC-ITS5 (50 -GGAAGGAGAAGTCGWAACARGG-30 ), and the universal indels. All analyses were performed with four independent runs
reverse primer ITS4 (50 -TCCTCCGCTTATTGATATGC-30 ; White et al., of Markov Chains Monte Carlo (MCMC) each with four parallel
1990). chains. Each chain was performed for 1 million generations, saving
PCR amplification was performed using the following reaction one random tree every 100th generation. The burn in was set to
mix: 1.5 mM MgCl2, 1X PeqLab Taq Buffer S (including MgCl2), 100,000, and a majority consensus tree was computed with the
0.25 mM each dNTP, 0.8 pmol primer, 0.03 U/ul Taq polymerase remaining trees.
(PeqLab, Erlangen Germany) and 0.8 ng/ul DNA template. For diffi- To test for congruence between the respective data sets, we ran
cult templates (e.g. DNA isolated from herbarium material), beta- the Incongruence Length Difference (ILD) test (Farris et al., 1994),
ine was added to a final concentration of 1 M. The PCR was implemented in PAUP⁄ as the Partition Homogeneity Test, and
performed in a T3 Thermocycler (Biometra, Göttingen, Germany) using the following parameters: 10,000 replicates with 50 Random
or a Mastercycler (Eppendorf, Hamburg, Germany). The PCR pro- Addition Searches, holding only two trees each step and saving no
gram used for the chloroplast region trnL-F was: 30 cycles of dena- more than 5 trees. The test was conducted for (i) the complete data
turation (60 s at 94 °C), annealing (60 s at 52 °C), extension (120 s set (140 taxa), (ii) a reduced data set including only diploid taxa,
at 72 °C) and a final extension step (15 min at 72 °C). The PCR pro- and (iii) for each of the well-supported major clades.
gram for the ITS region was: 35 cycles of denaturation (60 s at
97 °C), annealing (60 s at 48 °C), extension (45 s at 72 °C) and a fi-
3. Results
nal extension step (7 min at 72 °C). Primer dimers and secondary
banding patterns were separated from the requested bands using
3.1. The non-coding trnL–F chloroplast region
a 1.5% NEEO agarose gel (Carl Roth, Germany) running for 3 h at
100 volts. Gel extraction was performed using the AveGene
Sequence lengths varied from 304–643 nt in the intron and
Gel/PCR DNA Fragments Extraction Kit (AveGene life science Cor-
137–386 nt in the spacer. The aligned data set comprised 1240 char-
poration). The quality and quantity of the purified PCR product
acters including 345 (27%) that were parsimony informative. Seven
were measured with a NanoDrop spectrophotometer. Cycle
areas classified as ‘‘hotspots’’ (HS) sensu Borsch et al. (2003) were
sequencing, fragment purification, and direct automated sequenc-
excluded from the analyses (Appendix D). One inversion was found
ing was performed by Macrogen Inc. (Seoul, South Korea).
in the trnL intron in all samples of Krascheninnikovia (Appendix A).
The final matrix, including coded indels, comprised 1402 characters
2.3. Alignment and coding of length mutational events
of which 461 (33%) were parsimony informative. The MP search re-
sulted in 307 shortest trees (L = 1027, CI = 0.702, a RI = 0.933 and a
Sequences were edited and aligned manually using PhyDE
RC = 0.655). The resulting strict consensus tree was identical in
(Phylogenetic Data Editor) version 0.995 (Müller et al., 2007), fol-
topology with the Bayesian majority-rule consensus tree (see Fig. 1).
lowing the rules outlined in Löhne and Borsch (2005). Regions of
uncertain homology (mutational hotspots) were excluded from
the analysis (see Appendices A, B and D). Hypothesized microstruc- 3.2. The nuclear ITS region
tural mutations that explain the length variability patterns of se-
quences in the aligned partition are listed in Appendices A and B, Sequence lengths varied from 149–174 nt in ITS1 and 188–205
as suggested by Borsch et al. (2007), Morrison (2009) and Ochote- nt in ITS2. Both spacers were surprisingly well aligned except some
rena (2009). The inversions were re-inverted and coded as muta- sequence parts excluded as mutational hotspots (Appendix D). The
tional event in the indel matrix following Löhne and Borsch hotspot in ITS1 was on average 60 nt in length and the two hot-
(2005). Indels were then coded automatically using the Simple In- spots in ITS2 were 6 and 19 nt in length, respectively. Hypothe-
del Coding method (Simmons and Ochoterena, 2000) as imple- sized microstructural mutations are listed in Appendix B. Of all
mented in SeqState 1.40 (Müller, 2005a). The alignments are characters, 35% were parsimony informative, after indels were
available in TreeBase (Submission 11780). coded as binary characters and added to the matrix (687 characters
in total), the percentage of parsimony informative characters in-
2.4. Phylogenetic analyses creased to 39%. Parsimony analyses of the ITS region resulted in
1633 shortest trees (L = 939, CI = 0.502, RI = 0.890, RC = 0.446) with
Maximum Parsimony (MP) analyses were performed using the indels coded. Both MP and Bayesian analyses gave consensus trees
Parsimony Ratchet (Nixon, 1999) using the software PRAP (Müller, with identical topology (Fig. 2).
2004) in combination with PAUP⁄ v. 4.0b10 (Swofford, 1998).
Ratchet settings were 200 ratchet iterations with 25% of the posi- 3.3. Phylogenetic relationships
tions randomly up weighted (weight = 2) during each replicate
and 10 random addition cycles. MP and Bayesian analyses of the respective trnL-F and ITS data
The command files generated with PRAP were then run in PAUP, sets depict seven strongly supported clades (clades 1–7; Figs. 1
using the heuristic search with the following parameters: all char- and 2), encompassing both the Chenopodieae (clades 2–5, 7) and
acters have equal weight, gaps are treated as ‘‘missing’’, TBR branch the Atripliceae sensu stricto (clade 6). Clade 1 contains Axyris, Cerato-
swapping, initial swapping on 1 tree already in memory, Maxtrees carpus and Krascheninnikovia (maximum support in all trees) and
set to 100 (auto increased by 100) and branches collapsed actively either appears sister to the remaining Chenopodioideae (trnL-F;
if branch length is zero. The Jackknife (JK) support for branches was Fig. 1) or is inconsistently resolved among the early branching lin-
also performed in PAUP with 10,000 replicates, using a TBR branch eages of the Chenopodioideae (ITS). The genus Chenopodium itself
swapping algorithm with 36.788% of characters deleted and one is highly paraphyletic to nearly all other genera of the subfamily
tree held during each replicate, following Müller (2005b). and its species are distributed in five different well defined lineages
Bayesian inference (BI) was carried out using MrBayes 3.1 (clades 2–5 and 7; Figs. 1 and 2). Clade 2 (trnL-F 100% JK/1 PP, ITS 98%
(Huelsenbeck and Ronquist, 2001). Optimal nucleotide substitu- JK/1 PP) encompasses Ch. ambrosioides and a number of other aro-
tion models for the respective trnL–F (GTR + G) and ITS matic species as well as the monotypic genus Suckleya. Clade 3 re-
(GTR + G + I) data sets were chosen following the Akaike Informa- ceives high support with trnL-F (99% JK /1 PP) but only moderate
tion criterion (AIC) in Modeltest 3.7 (Posada and Crandall, 1998). support in the ITS tree (67% JK/1 PP). It comprises Chenopodium bo-
A binary (restriction site) model was implemented for the coded nus-henricus and relatives and Monolepis in one subclade and all spe-
S. Fuentes-Bazan et al. / Molecular Phylogenetics and Evolution 62 (2012) 359–374 363
Table 2
Samples included in this study.
Taxon Field/Garden origin Voucher Code trnL-F Acc. ITS Acc.

Subfamily Chenopodioideae
Tribe Atripliceae C. A. Meyer
Atriplex hortensis L. Estonia, Tallin Gawe 41350 (B) AC516 HE577500 HE577360
Atriplex patula L. Germany, Brandenburg R. & E. Willing 20.836 (B) AC605 HE577498 HE577358
Atriplex sagittata Borkh. Berlin Bot. Gard. No: 063119110 S. Fuentes 021 (B) AC533 HE577499 HE577359
[Germany]
Atriplex nitens Schkuhr Germany, Brandenburg R. & E. Willing 10.701 D (B) AC573 HE577501 HE577361
Stutzia dioica (Nutt.) E.H. Zacharias USA L. Welp 6269 (NY) AC351 HE577502 HE577362
Grayia spinosa (Hook.) Moq. USA ARS GRIN W626763 [USA, S. Fuentes 177 (B) AC625 HE577496 HE577356
California]
Grayia brandegeei A. Gray USA ARS GRIN W630044 [USA, S. Fuentes 179 (B) AC627 HE577497 HE577357
Colorado]
Microgynoecium tibeticum Hook. f. China B. Dickoré 4284 (B) AC656 HE577503 HE577363
Tribe Axyrideae G. Kadereit & Sukhorukov
Axyris amaranthoides L. Russia L. Martins 2346 (B) AC647 HE577510 HE577370
Axyris hybrida L. Russia L. Martins 2417 (B) AC648 HE577511 HE577371
Axyris prostrata L. Russia E. v. Raab-Straube 020232a (B) AC529 HE577509 HE577369
Ceratocarpus arenarius L. Romania, Navodari A. Romanovsch (B) AC531 HE577504 HE577364
Ceratocarpus arenarius L. Russia L. Martins 2447 (B) AC649 HE577505 HE577365
Krascheninnikovia ceratoides (L.) Gueldenst. Russia L. Martins 2500 (B) AC608 HE577506 HE577366
Krascheninnikovia ceratoides (L.) Gueldenst. Russia R. Hand 1536 (B) AC532 HE577507 HE577367
Krascheninnikovia lanata (Pursch) A. Meeuse & A. Smit USA ARS GRIN W629970 [USA, S. Fuentes 178 (B) AC626 HE577508 HE577368
Colorado]
Tribe Dysphanieae Pax
Suckleya suckleyana (Torr.) Rydb. USA R. Darn 5373 (NY) AC350 HE577484 HE577347
sect. Ambrina (Spach.) Hook
Chenopodium ambrosioides L. Bolivia, Beni I. Guareco 420 (B, LPB) AC420 HE577492 HE577352
Chenopodium ambrosioides L. Bolivia, La Paz S. G. Beck 31178 (B, LPB) AC425 HE577493 HE577353
Chenopodium ambrosioides L. Berlin Bot. Gard. No: S. Fuentes 024 (B) AC527 HE577491 HE577351
10095019310 [Italy]
Chenopodium ambrosioides L. Ethiopia M. Wondafrash 2223 (B, ETH) AC386 HE577488 HE577350
[=Dysphania ambrosioides (L.) Mosyakin & Clemants]
sect. Botryoides C. A. Meyer
subsect. Botrys (Koch) Aellen et Iljin
Chenopodium schraderianum Schult. Ethiopia M. Wondafrash 2255 (B, ETH) AC387 HE577490 HE577349
Chenopodium graveolens Willd. Bolivia E. Thomas 258 (B, LPB) AC419 HE577495 HE577355
[=Dysphania graveolens (Wlld.) Mosyakin & Clemants]
subsect. Teloxys (Moq.) Aellen et Iljin
Chenopodium aristatum L. Berlin Bot. Gard. No: 309669170 S. Fuentes 025 (B) AC528 HE577480 HE577340
[Germany]
Chenopodium aristatum L. Russia L. Martins 2377 (B) AC610 HE577479 HE577339
Chenopodium aristatum L. USA ARS GRIN Ames 25314 S. Fuentes 183 (B) AC654 HE577481 HE577341
[=Teloxys aristata (L.) Moq.] [Mongolia]
sect. Orthosporum R. Br.

Chenopodium melanocarpum (J.M. Black) J.M. Black. Australia C.R. Michael & J. Risles 1921 (B) AC429 HE577487 HE577344
[=Dysphania melanocarpa (J.M. Black) Mosyakin &
Clemants]
Chenopodium pumilio R. Br. Germany T. Borsch (B) AC524 HE577486 HE577343
Chenopodium pumilio R. Br. Greece R. & E. Willing 85.571 (B) AC604 HE577485 HE577342
Chenopodium pumilio R. Br. Mexico T. Borsch (B) AC615 HE577489 HE577348
[=Dysphania pumilio (R. Br.) Mosyakin & Clemants]
Tribe Chenopodieae
Einadia nutans (R. Br.) A. J. Scott. Berlin Bot. Gard. No: 187199 S. Fuentes 019 (B) AC525 HE577553 HE577415
[Australia]
Monolepis nuttalliana (Schult.) Greene USA, Utha R. C. Holmgren 317 (B) AC621 HE577515 HE577375
Rhagodia triandra (G.Forst.) Aellen New Zealand P. Hein 12560 (B, CHR) AC522 HE577554 HE577416
Chenopodium L.
Subgen. Ambrosida
sect. Botryoides C. A. Meyer
subsect. Botrys (Koch) Aellen et Iljin
Chenopodium coronopus Moq. Spain, La Palma Royl 6823 (B) AC570 HE577543 HE577403
Subgen. Blitum
sect. Degenia Aellen
Chenopodium chenopodioides (L.) Aellen USA, Montana P. C. Lesica 5792 (NY) AC543 HE577519 HE577379
sect. Pseudoblitum Hook
subsect. Glaucum Aellen
Chenopodium glaucum L. USA ARS GRIN PI612859 [USA] S. Fuentes 184 (B) AC652 HE577526 HE577386
Chenopodium glaucum L. Spain T. Borsch 3931 (B) AC417 HE577527 HE577387
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Table 2 (continued)

subsect. Viride Aellen
Chenopodium rubrum L. Germany, North See T. Borsch [08.07] (B) AC411 HE577520 HE577380
Chenopodium rubrum L. Germany E. Willing 10.931D (B) AC564 HE577522 HE577382
Chenopodium rubrum L. USA ARS GRIN Ames 23860 S. Fuentes 182 (B) AC653 HE577521 HE577381
[Poland]
Chenopodium rubrum L. USA T. Borsch 3448 (B) AC385 HE577525 HE577385
Subgen. Chenopodium
sect. Chenopodium Aellen
subsect. Cellulata Aellen
Chenopodium berlandieri Moq. USA, Nevada J. C. Beatley 11698 (NY) AC541 HE577561 HE577423
Chenopodium berlandieri Moq. USA, Colorado G. Rink 2527 (NY) AC599 HE577567 HE577429
Chenopodium berlandieri var. boscianum (Moq.) Wahl USA, Lousiana D. M. Ferguson 1072 (NY) AC545 HE577564 HE577426
Chenopodium berlandieri subsp. nuttalliae (Saff.) H.Dan. Mexico T. Borsch & H. Flores Olvera (B, AC616 HE577565 HE577427
Wilson & Heiser MEXU)
Chenopodium berlandieri var. zschackei (Murr) Murr ex USA, Colorado C. C. Freeman 16479 (NY) AC542 HE577563 HE577425
Graebn.
Chenopodium berlandieri var. zschackei (Murr) Murr ex USA, Wyoming A. J. Roderick 2286 (NY) AC600 HE577569 HE577431
Graebn.
Chenopodium ficifolium Sm. Germany, Berlin R. & E. Willing 12.260 D (B) AC854 HE577606 HE577466
Chenopodium quinoa Willd. USA ARS GRIN Ames 13214 S. Fuentes 013 (B) AC401 HE577580 HE577445
[Bolivia]
Chenopodium quinoa Willd. USA ARS GRIN Ames 13228 S. Fuentes 017 (B) AC402 HE577576 HE577441
[Ecuador]
Chenopodium quinoa Willd. USA ARS GRIN PI568155 [Mexico] S. Fuentes 015 (B) AC403 HE577581 HE577446
Chenopodium quinoa Willd. USA ARS GRIN PI510551 [Peru] S. Fuentes 009 (B) AC404 HE577579 HE577444
Chenopodium quinoa Willd. USA ARS GRIN PI587173 S. Fuentes 012 (B) AC405 HE577577 HE577442
[Argentina]
Chenopodium quinoa Willd. USA ARS GRIN PI596498 [Peru] S. Fuentes 008 (B) AC406 HE577578 HE577443
Chenopodium quinoa Willd. USA ARS GRIN PI614880 [Chile] S. Fuentes 010 (B) AC407 HE577582 HE577447
Chenopodium quinoa Willd. USA ARS GRIN PI614914 [Bolivia] S. Fuentes 011 (B) AC408 HE577583 HE577448
Chenopodium quinoa Willd. USA ARS GRIN PI568155 [Mexico] S. Fuentes 016 (B) AC394 HE577571 HE577433
Chenopodium neomexicanum Standl. USA, New Mexico R.D. Worthington 13394 (NY) AC555 HE577611 HE577471
Chenopodium neomexicanum Standl. USA, Arizona S. Fuentes 172 (B) AC598 HE577601 HE577461
Chenopodium pallescens Standl. USA, Missouri G. Yatskievych 03–93 (MO) AC594 HE577547 HE577409
Chenopodium pallescens Standl. USA, Illinois T.G. Lammers 10336 (NY) AC557 HE577604 HE577464
Chenopodium watsonii A. Nelson USA, Arizona D.H. Goldman 2095 (NY) AC561 HE577602 HE577462
subsect. Grossefoveata Aellen
Chenopodium hybridum L. Germany T. Borsch 3897 (B) AC380 HE577530 HE577390
Chenopodium hybridum L. Russia, Altay Republic L. Martins 2329 (B) AC609 HE577528 HE577388
Chenopodium hybridum L. Germany, Brandenburg R. & E. Willing 20.856 D (B) AC521 HE577529 HE577389
Chenopodium gigantospermum var. standleyanum USA, Kansas C.A. Morse 10855 (NY) AC550 HE577551 HE577413
Aellen
subsect. Lejosperma Aellen
Chenopodium album L. Greece, Messinia R. & E. Willing 122.544 (B) AC571 HE577558 HE577420
Chenopodium album L. Germany, Usedom Weber (B) AC602 HE577559 HE577421
Chenopodium album L. Russia, Altay Republic E. v. Raab-Straube 020350 (B) AC575 HE577609 HE577469
Chenopodium album L. Germany, Bonn S. Fuentes 001 (B) AC388 HE577557 HE577419
Chenopodium album L. Spain T. Borsch 3921 (B) AC414 HE577592 HE577453
Chenopodium album L. USA ARS GRIN PI608030 [USA] S. Fuentes 007 (B) AC395 HE577568 HE577430
Chenopodium album L. USA ARS GRIN Ames 27372 [USA] S. Fuentes 006 (B) AC396 HE577570 HE577432
Chenopodium album L. Spain T. Borsch 3921 (B) AC427 HE577593 HE577456
Chenopodium album L. Russia, Altay Republic L. Martins 2423 (B) AC614 HE577552 HE577414
Chenopodium album L. USA, Arizona H.D. Hammond 11926 (MO) AC591 HE577596 HE577457
Chenopodium album L. USA, Wisconsin N.J. Holmberg 1976 (MO) AC590 HE577556 HE577418
Chenopodium atrovirens Rydb. Bolivia, La Paz S.G. Beck 11328 (B, KAS, LPB) AC363 HE577586 HE577450
Chenopodium atrovirens Rydb. Bolivia, La Paz S.G. Beck 8377 (B, LPB) AC421 HE577587 HE577452
Chenopodium atrovirens Rydb. USA, Utha M. Madsen 40772 (MO) AC586 HE577584 HE577449
Chenopodium atrovirens Rydb. USA, Colorado T.G. Lammers et al. 11321 (NY) AC540 HE577585 HE577451
Chenopodium cycloides A. Nelson USA T. Borsch, Müller and Pratt 3452 AC384 HE577598 HE577459
(B)
Chenopodium cycloides A. Nelson USA, Kansas C.C. Freeman 2549 (NY) AC544 HE577599 HE577460
Chenopodium desiccatum A. Nelson USA, Missouri B. Summers & Harris 9813 (MO) AC588 HE577550 HE577412
Chenopodium fremontii S. Watson USA, California G. Schoolcraft 2206 (UC) AC579 HE577546 HE577408
Chenopodium fremontii S. Watson USA. Utha S. Fuentes 185 (B) AC597 HE577572 HE577436
Chenopodium giganteum D. Don Bonn Bot. Gart. No: 21397 [India] S. Fuentes 014 (B) AC428 HE577597 HE577458
Chenopodium hians Standl. USA, Wyoming S. Stephens 70636 (NY) AC551 HE577610 HE577470
Chenopodium incanum (S. Watson) A. Heller USA, New Mexico R. D. Worthington 17439 (NY) AC553 HE577548 HE577410
Chenopodium iljinii Golosk. Russia, Altay Republic L. Martins 2490 (B) AC611 HE577608 HE577468
Chenopodium iljinii Golosk. Russia, Altay Republic L. Martins 2424 (B) AC613 HE577607 HE577467
Chenopodium leptophyllum (Moq.) Nutt. ex S. Watson USA, Montana P.C. Lesica 8846 (NY) AC554 HE577566 HE577428
Chenopodium nevadense Standl. USA, Nevada A. Tiehm 13320 (NY) AC556 HE577549 HE577411
Chenopodium opulifolium Schrad. ex W.D.J. Koch & Ziz Slovakia T. Borsch 3899 (B) AC410 HE577595 HE577455
Chenopodium opulifolium Schrad. ex W.D.J. Koch & Ziz Spain T. Borsch 3926 (B) AC416 HE577594 HE577454
Chenopodium pallidicaule Aellen USA ARS GRIN PI478406 [Bolivia] No Voucher AC398 HE577574 HE577439
Table 2 (continued)

Chenopodium pallidicaule Aellen USA ARS GRIN PI510525 [Peru] No Voucher AC399 HE577573 HE577438
Chenopodium pallidicaule Aellen USA ARS GRIN PI 510530 [Peru] No Voucher AC400 HE577575 HE577440
Chenopodium pallidicaule Aellen Bolivia, Tarija S. G. Beck 31939 (B, LPB) AC426 HE577600 HE577437
Chenopodium pratericola Rydb. USA, Wyoming K. H. Dueholm 10922 (B, LPB) AC558 HE577562 HE577424
Chenopodium petiolare Kunth Bolivia, Oruro R. de Michel 2873 (B, KAS, LPB) AC359 HE577588 HE577434
Chenopodium petiolare Kunth Bolivia, La Paz S. G. Beck 22972 (B, LPB) AC423 HE577589 HE577435
Chenopodium standleyanum Aellen USA, Missouri A. E. Brant & R. Jefferson 4450 AC595 HE577560 HE577422
(MO)
Chenopodium standleyanum Aellen USA, Missouri N. J. Holmberg 554 (MO) AC596 HE577603 HE577463
Chenopodium subglabrum (S. Watson) A. Nelson USA, Wyoming R. D. Dorn 5434 (NY) AC559 HE577605 HE577465
Chenopodium urbicum L. Greece, Fthiotis R. & E. Willing 146.1979 (B) AC576 HE577524 HE577384
Chenopodium urbicum L. Berlin Bot. Gard. No: 269400010 S. Fuentes 026 (B) AC536 HE577523 HE577383
[Greece]
Chenopodium vulvaria L. Spain T. Borsch 3918 (B) AC412 HE577591 HE577407
Chenopodium vulvaria L. Greece, Evrytania R. & E. Willing 148.759 (B) AC562 HE577590 HE577406
subsect. Undata Aellen
Chenopodium murale L. Bolivia, La Paz S. G. Beck 22970 (B, KAS, LPB) AC360 HE577538 HE577398
Chenopodium murale L. Chile T. Borsch 3097 (B) AC383 HE577539 HE577400
Chenopodium murale L. USA ARS GRIN Ames 26140 [USA] S. Fuentes 005 (B) AC397 HE577534 HE577394
Chenopodium murale L. Spain T. Borsch 3919 (B) AC413 HE577535 HE577395
Chenopodium murale L. Spain T. Borsch 3924 (B) AC415 HE577536 HE577396
Chenopodium murale L. Bolivia, La Paz S. G. Beck 145PG94 (B, LPB) AC424 HE577537 HE577397
Chenopodium murale L. Slovakia T. Borsch 3915 (B) AC409 HE577533 HE577391
Chenopodium murale L. Greece, Korinthias R. & E. Willing 143.462 (B) AC430 HE577540 HE577399
Chenopodium murale L Mexico, Ixtapan T. Borsch & H. Flores Olvera 3871 AC382 HE577541 HE577401
(B, MEXU)
Chenopodium murale L. USA, California C. Dietrich et al. 32 (MO) AC589 HE577531 HE577392
Chenopodium murale L. Greece, Evvia R. & E. Willing 145.733 (B) AC566 HE577532 HE577393
Chenopodium murale L. Greece R. & E. Willing 145.592 (B) AC565 HE577542 HE577402
Chenopodium murale L. USA, California T. Ross 4084 (UC) AC581 HE577544 HE577404
Chenopodium murale L. USA, California G. Gust & L. Nyle 476 (MO) AC587 HE577545 HE577405
sect. Desertorum Wilson
Chenopodium desertorum subsp. anidiophyllum (Aellen) Australia C. Michaell & J. Risler 1773 (B, NT) AC519 HE577555 HE577417
P.G. Wilson
sect. Roubieva Rouy
Chenopodium multifidum L. Greece, Florina R. & E. Willing 85631 (B) AC574 HE577494 HE577354
[=Dysphania multifida (L.) Mosyakin & Clemants]
Tribe Spinaceae Moq. (this study)

sect. Agathophyton Hook
Chenopodium bonus-henricus L. Austria T. Borsch 3821 (B) AC381 HE577512 HE577372
Chenopodium californicum (S. Watson) S. Watson. USA, California P. Davis & D. Lightowless 66504 AC431 HE577516 HE577376
(B)
sect. Eublitum (Moq.) Aellen
subsect. Capitata Kowal ex Mosyakin and
Clemants
Chenopodium capitatum (L.) Ambrosi Bonn Bot. Gart. No: 19116 S. Fuentes 004 (B) AC391 HE577513 HE577373
Chenopodium capitatum var. parvicapitatum S.L. Welsh USA, Utha K. Moon et al. 1993 (NY) AC547 HE577514 HE577374
Spinacia oleracea L. AJ400848.1
Spinacia oleracea L. EU606218.1
Spinacia tetrandra Steven ex M. Bieb. USA ARS GRIN Ames 23664 [Asia] S. Fuentes 180 (B) AC650 HE577482 HE577345
Spinacia turkestanica Iljin USA ARS GRIN Ames 23666 [Asia] S. Fuentes 181 (B) AC651 HE577483 HE577346
subsect. Foliosa Kowal ex Mosyakin and Clemants
Chenopodium foliosum Asch. Bonn Bot Gart No: 19117 S. Fuentes 003 (B) AC392 HE577517 HE577377
[Germany]
Chenopodium foliosum Asch. Kirgistan, Central Asia Cubr 42389 (B) AC520 HE577518 HE577378
OUTGROUPS
Subfamily Betoideae Ulbr.
Beta vulgaris subsp. maritima (L.) Thell. Denmark, Jylland Cubr 39900 (B) AC530 HE577473 HE577334
Hablitzia tamnoides M. Bieb. Germany, Bonn Bot. Gard No: No Voucher AC018 HE577475 -
03609–90
Hablitzia tamnoides M. Bieb. Germany, Berlin Bot Gard No: S. Fuentes 018 (B) AC523 HE577474 HE577335
16611
Hablitzia tamnoides M. Bieb. AY858590.1
Subfamily Camphorosmoideae Luerss.

Bassia laniflora (S.G. Gmel.) A.J. Scott Germany, Berlin Bot Gard No: S. Fuentes 022 (B) AC534 HE577476 HE577336
17809970
Bassia scoparia (L.) A.J. Scott Russia L. Martins 2295 (B) AC607 HE577477 HE577337
Bassia prostrata (L.) A.J. Scott Russia L. Martins 2429 (B) AC606 HE577478 HE577338
(continued on next page)

Table 2 (continued)

Subfamily Salicornideae Ulbr.
Allenrolfea vaginata Kuntze Germany, Bonn Bot Gard No: AC017 HE577472 -
2488
Allenrolfea occidentalis Kuntze AY181875.1
Note: The circumscription of subfamilies in Chenopodiacae follows the tree annotations in Kadereit et al. (2003); within Chenopodioideae the tribes Atripliceae, Axyrideae
and Dysphanieae are recognized based on Kadereit et al. (2010); Spinacieae are listed as resurrected here; remaining genera are included into Chenopodieae (Kühn, 1993)
using the infrageneric classification of Chenopodium by Aellen (1960) except the members of Dysphanieae and Wilson (1983) for sect. Desertorum of Chenopodium. USA ARS
GRIN refers to USDA, ARS, National Genetic Resources Program. Germplasm Resources Information Network - (GRIN). [Online Database] National Germplasm Resources
Laboratory, Beltsville, Maryland.
cies of Spinacia in another. The monophyly of Spinacia (trnL-F 100% fied by the respective positions of clades 1, 2 and 3 (Ayridae, Dys-
JK/1 PP, ITS 100% JK/1 PP) is supported here for the first time. Clade phanieae, Spinacieae; Figs. 1 and 2) or the position of Ch.
4 (trnL-F 100% JK/1 PP, ITS 100% JK/1 PP) is composed of Ch. rubrum opulifolium within clade 7. In the first example incongruence is soft
and a number of other species (Ch. rubrum clade) and clade 5 (no statistic confidence in deviating topologies) whereas it is hard
(trnL-F 100% JK/1 PP, ITS 83% JK/1 PP) contains Chenopodium murale, (well supported nodes differ) in the second case. Causes for incon-
Ch. hybridum and relatives (Ch. murale clade). Finally, clade 7 (trnL-F gruence are manifold, and can be either of non-biological (e.g.
100% JK/1 PP, ITS 88% JK/1 PP) embraces most of the other Chenopo- insufficient taxon sampling, long-branch attraction, etc.) or biolog-
dium species, along with the genera Einadia and Rhagodia. The ical (e.g. incomplete linage sorting, orthology/paralogy conflation,
remaining clades 1 and 6 only include taxa from the former Atripli- or hybridization) origin (Wendel and Doyle, 1998; Sanderson
ceae sensu lato. While clade 6 (trnL-F 97% JK/1 PP, ITS 50% JK/0.65 et al., 2000).
PP) encompasses Atriplex, Stutzia, Grayia and Microgynoecium, the On the one hand, the extent of our current taxon sampling
maximally supported clade 1 consists of Axyris, Ceratocarpus and (more than 135 taxa representing the diversity of Chenopodium
Krascheninnikovia. sensu lato) and the similar topologies obtained from both MP
and Bayesian analyses of the respective markers allow us to reject
3.4. Phylogenetic incongruence with confidence most analytical causes of topological incongru-
ence. Indeed, it has been recently demonstrated that an increase
The ILD test showed strong incongruence between the respec- of taxon sampling in a Bayesian context tends to decrease the risk
tive partitions of the data sets, even in the absence of polyploid of erroneous topologies due to long-branch attraction (Van der
taxa (P < 0.001). When clades were compared separately, topolog- Niet and Linder, 2008). Furthermore, incomplete lineage sorting
ical incongruence was also detected within clades 2, 3, 4 and 7 of the ITS alleles can be excluded as a cause of topological conflict
(P < 0.001), but not for clades 1, 5, and 6 (P = 1, excluding Microgy- due to the absence of polymorphic sites in all direct sequences
noecium due to its unclear phylogenetic position). The position of investigated. Yet, this lack of ITS polymorphism does not allow
the three first branching lineages in Chenopodioideae differs be- us to identify potential additive polymorphic sites, which would
tween ITS and trnL-F. In the ITS tree, deep nodes are unsupported support past hybridization events (Nieto Feliner et al., 2001; Man-
in MP and only clade 1 as third branching is supported by a PP of sion et al., 2005; Guggisberg et al., 2009).
1. Clade 4 and 5 are resolved either as sister lineages (ITS 82% JK/ We are aware that we cannot clearly discriminate between
0.91 PP) or in a grade (trnL-F). Within clade 7, resolution is poor orthology/paralogy conflation and reticulation patterns in the ab-
but individual samples (e.g. Ch. ficifolium) are inferred incongru- sence of extensive cloning of the ITS region, especially in clades
ently in the chloroplast and nuclear trees. with low interspecific resolution (e.g. clade 7, Figs. 1 and 2). A more
detailed study, taking into account the current limitations of our
4. Discussion current molecular data set, and using non-molecular evidence
based on caryology, morphology, and phytochemistry is underway.
This study is based on the most extensive sampling of Chenopo- Overall, we feel that it is more appropriate to individually dis-
dium species to date. By using the highly variable non-coding cuss evolutionary and taxonomic implications of trees inferred
trnL-F (cpDNA) and ITS (nrDNA) regions, we provide the first com- from organellar and nuclear genomic compartments, especially
prehensive phylogeny of this controverted large genus. Overall, we when sources of potential incongruence remain unclear. Further-
support the highly paraphyletic status of Chenopodium, as sug- more, such an approach allows us to compare the phylogenetic
gested by Kadereit et al. (2003) and Müller and Borsch (2005), utility of the respective data partitions.
and reveal new well-supported lineages, resolved with high confi-
dence (Figs. 1 and 2). Because of this paraphyly, our results also af- 4.2. Phylogenetic utility of the trnL-F and ITS regions
fect the picture of the subfamily Chenopodioideae. Whereas the
studies by Kadereit et al. (2003, 2010) suggested three of the five The use of non-coding and rapidly evolving genomic regions
lineages of Chenopodium s.l. (Chenopodieae I, II, III; Chenopodieae from the chloroplast genome in angiosperm phylogenetics has
III were already called Dysphanieae in Kadereit et al., 2010), our re- been accelerating during recent years. Following initial proposals
sults offer further support and resolution of these lineages and (e.g. Taberlet et al., 1991), it has been demonstrated that not only
identify two novel major clades (Ch. murale and relatives, Ch. ru- the percentage of variable sites, and thus the quantity of informa-
brum and relatives) out of the Chenopodieae I. Our data also pro- tion, but also the quality of phylogenetic signal of non-coding re-
vide statistical support for the Chenopodieae II, which we gions outperforms more conserved coding genes such as rbcL
recognize as Spinacieae. (Borsch et al., 2003; Müller et al., 2006). One of the major insights
is that chloroplast DNA mutational dynamics follows certain prin-
4.1. Congruence of data partitions ciples across genomic regions and taxa (see Borsch and Quandt,
2009 for a summary). As a consequence, motif based alignment al-
Different combinations on the ILD test reveal some topological lows more precise homology statements (Morrison, 2009;
incongruence between the respective data partitions, as exempli- Ochoterena, 2009), although, on the other hand mutational hot-
Fig. 1. Bayesian majority rule tree based on the sequence dataset of trnL-F including coded indels. Bayesian posterior probabilities (pp) are given above and Jackknife (JK)
values below branches. The abbreviations following species names in parentheses refer to the sections and subsections proposed for Chenopodium by Aellen (1960);
(Ag) = Sect. Agathophyton, (Am) = sect. Ambrina, (Bo) = sect. Botryoides; the sect. Chenopodium is represented by (Ce) = subsect. Cellulata, (Gr) = subsect. Grossefoveata,
(Le) = subsect. Lejosperma, and (Un) = subsect. Undata; further sections are (De) = sect. Degenia, (Eu) = sect. Eublitum, (Or) = sect. Orthosporum, (Pse) = sect. Pseudoblitum, and
(Ro) = sect. Roubieva. The second column of clade annotations refers to the accepted subgenera of Chenopodium (Judd and Ferguson, 1999), and the third column to tribe
names accepted in this study as explained in Fig. 2.
Fig. 2. Bayesian majority rule tree based on the sequence dataset of nrITS including coded indels. Bayesian posterior probabilities (pp) are given above and Jackknife (JK)
values below branches. Boxes in gray mark the genera Dysphania and Teloxys from the Dysphanieae that are now accepted as genera distinct from the former Chenopodium
sensu lato, and the representatives of the former genera Einadia and Rhagodia that are included into Chenopodium s.str. (clade 7) in this study. The second column refers to
tribe names Spinacieae (newly resolved in this study), Atripliceaea, Axyrideae and Dysphanieae (sensu Kadereit et al. (2010) and Zacharias and Baldwin (2010); supported in
this study); and for Chenopodieae the newly Chenopodium s.str, Ch. murale lineage and Ch. rubrum linegae found in this study.
spots of unclear homology have to be excluded even in data sets Suckleya suckleyana, previously placed in the Atripliceae sensu lato
representing species level diversity within genera. This study pro- (Kühn, 1993), is resolved with high confidence (99% JK/1 PP) as sister
vides a further example for this (seven mutational hotspots in the group to all other species of aromatic Chenopodium except Ch. arist-
trnL-F region of Chenopodium s.l.). The current trnL-F data set is one atum (= Teloxys aristata).
of the largest so far generated for a family of Caryophyllales. Our results corroborate a recent tree based on rbcL (Kadereit
Previous workers used the trnL-F region, due to its high variability et al., 2010) and also find Suckleya in a position sister to a number
compared to other chloroplast markers in Suaeda, Salicornia and al- of Dysphania species, clearly apart of the Atripliceae clade. Suckleya
lies, or Beta and allies (Kapralov et al., 2006; Murakeözy et al., shares ebracteolate flowers with the aromatic chenopods, but dif-
2007; Hohmann et al., 2006). The first molecular analysis of the fers by being monoecious and by its female perianth which be-
Amaranthaceae–Chenopodiaceae alliance by Kadereit et al. comes winged when mature (Chu et al., 1991). It is thus justified
(2003) was based on sequences of the rbcL gene, but the resulting to maintain it as a separate genus distinct from the other aromatic
trees were largely unresolved at deeper nodes and lacked statisti- species of Chenopodium (= Dysphania spp.). To confirm the presence
cal support in many parts. A subsequent analysis by Müller and of glandular trichomes as a putative synapomorphy for clade 2, it
Borsch (2005) used trnK/matK plastid data, and generated a much will be necessary to revisit the fine structure of Suckleya trichomes
improved phylogenetic hypothesis for Amaranthaceae and Cheno- and to confirm their glandular nature. Nevertheless, available data
podiaceae. Remarkably, the trnL-F region (composed of the trnL (Chu et al., 1991) show that the inflated unicellular trichomes of
gene with its group I intron and the trnL–trnF intergentic spacer; Suckleya appear to be similar to the Type I trichomes found in other
e.g. Quandt et al., 2004) is about half the size of matK/trnK and aromatic species of Chenopodium (= Dysphania spp.; Bonzani et al.,
yields the so far best resolved and supported tree of a major Cheno- 2003). The three samples representing geographically different
podiaceae lineage. This is paralleled by trnL-F trees from the spec- populations of Ch. aristatum appear as sister group (100% JK/ 1
iose subfamily Gomphrenoideae of the Amaranthaceae (Sánchez PP) to the remainder of the species in clade 2. This species also dif-
del Pino et al., 2009), suggesting that trnL-F should be employed fers morphologically by having dichasial inflorescences (Moquin-
as a standard marker in Amaranthaceae–Chenopodiaceae. Tandon, 1840; Weber, 1985) and bristle-tipped terminal inflores-
The nuclear, biparentally inherited internal transcribed spacer re- cence branches (Mosyakin and Clemants, 2002, 2008) that would
gion (ITS1, 5.8S, ITS2) yields trees that essentially show the same se- support its recognition as a distinct genus Teloxys. It should be
ven major lineages. Only some nodes, especially at deeper parts of the noted that this circumscription of Teloxys corresponds to the con-
tree, are weakly supported and inconsistently resolved (see Clades 1, cept of the genus held by Ulbrich (1934) or of subsect. Teloxys (of
2 and 3, Fig. 2). This pattern may be explained because ITS evolves dif- Dysphania sect. Dysphania) proposed by Mosyakin and Clemants
ferently to chloroplast regions. Motifs for microstructural changes (2002), respectively.
are less evident. In fact, most mutations (see indel character list; Clade 3 is strongly supported by trnL-F (Fig. 1; 99% JK/1 PP) to
Appendix B) appear to be mostly deletions or insertions of single comprise several Chenopodium spp., Monolepis and Spinacia but
nucleotides. Occurring repeatedly at greater distances, this may ob- has only moderate support in the ITS tree (67% JK, Fig. 2). It corre-
scure sequence divergence caused by substitutions, leading to less ro- sponds to ‘‘Chenopodieae II’’ sensu Kadereit et al. (2003, 2010) that,
bust homology assessments, in addition to potential effects of however, was not recovered with statistic confidence in their pre-
concerted evolution of many ITS copies (see Álvarez and Wendel, viously published rbcL tree. ‘‘Chenopodieae II’’ as depicted here
2003; Nieto Feliner and Rosselló, 2007). Some parts of the ITS tree (Figs. 1 and 2) lacks clear morphological synapomorphies except
are clearly incongruent (see Fig. 2) to the chloroplast tree. This sug- the presence of dense, head-like glomerules on terminal or axillary
gests reticulate patterns which could be explained by patterns of spe- branches. Within this clade, a Spinacia lineage is highly supported
ciation. The deep topological differences are rather inconsistent (low by both DNA markers (100 JK, Figs. 1 and 2) as sister to the remain-
support) and this can be explained by intrinsic patterns of molecular ing taxa, and comprises all Spinacia species described so far (Kühn,
evolution. 1993; Welsh et al., 2003). The Spinacia subclade is further charac-
terized by the presence of unisexual flowers without perianth, not
4.3. Paraphyly of Chenopodium L. found in the sister lineage comprising Ch. capitatum, Ch. californi-
cum, Ch. bonus-henricus, Ch. foliosum and Monolepis nuttalliana.
Both MP and Bayesian analyses based on DNA markers of differ- The latter all have bisexual flowers and a differentiated perianth.
ent genomic compartments (cp- and nrDNA) support the para- Our data strongly refute a previous hypothesis of a sister group
phyly of the genus as currently described, and further the relationship between Spinacia oleracea and Monolepis nuttaliana
inclusion of all the investigated species of Chenopodium into five that was found based on rbcL sequences (Kadereit et al., 2003),
different clades (Figs. 1 and 2). For clarity, the name Chenopodium but agree with the recently suggested exclusion of Spinacia from
is used throughout for all species it has been applied to over time Atripliceae (Kadereit et al., 2010).
(Figs. 1 and 2). The Chenopodium rubrum clade (Clade 4; Figs. 1 and 2) is new-
A clade containing aromatic species of Chenopodium (clade 2, see ly resolved here based on both trnL-F and ITS with maximum
below ‘‘Dysphanieae’’), is highly supported (Figs. 1 and 2), and is confidence. It encompasses Chenopodium chenopodioides, Ch. glau-
either resolved as a first or second diverging lineage of Chenopodium cum, Ch. rubrum and Ch. urbicum. Whereas chloroplast sequences
s.l., depending on whether ITS or trnL-F are analysed. It comprises Ch. suggest its placement in a grade branching after the Chen-
ambrosioides, Ch. graveolens, Ch. melanocarpum, Ch. multifidum, Ch. opodieae II (=Spinacieae; see Fig. 1), nuclear ITS data provide
pumilio, Ch. schraderianum, and Ch. aristatum, which all share the some evidence for the clade being sister to a Ch. murale clade
presence of specialized aromatic glandular hairs (‘‘type 8’’; Carolin, (Clade 4; Fig. 2). Based on the available morphological data, mor-
1983; Bonzani et al., 2003), as well as Suckleya suckleyana which phological synapomorphies for this clade are not clear at this
has inflated unicellular trichomes (Chu et al., 1991). Our data sup- point. Flowers with 3–4 perianth segments are shared by Ch. ru-
port the previous proposal by Carolin (1983) and Mosyakin and brum and Ch. glaucum, whereas flowers of Ch. chenopodioides con-
Clemants (1996) to separate aromatic chenopods with glandular sistently present only three segments, and those of Ch. urbicum
hairs under the generic name Dysphania (including Teloxys in this have five segments. Moreover, a reddish seed coat is shared by
genus) from the remaining ones (possessing bladder or sub-stellate Ch. rubrum, Ch. glaucum and Ch. urbicum, whereas Ch. chenopodio-
hairs), and denote the importance of hair types as characters for the ides has seeds with a black coat. Inflorescences with subglobose
systematics of Chenopodioideae. Within the aromatic clade, glomerules are present in all these taxa and seem to be a
synapomorphy. Nevertheless, this character is homoplastic within with numerous North American diploid species. Nonetheless, res-
Chenopodioideae (Iljin, 1936; Aellen, 1960; Welsh et al., 2003). olution within this major Chenopodium clade in the ITS tree is
Looking at the sectional level within Chenopodium, (based on even worse than in the chloroplast tree (Fig. 2).
Aellen and Just, 1943 and Aellen, 1960) this clade is composed
of members of section Pseudoblitum (Ch. rubrum and Ch. glaucum) 4.4. Circumscription and phylogenetic position of the tribes Atripliceae
that is morphologically similar to section Degenia (Aellen and Just, and Axyrideae
1943), here represented by Ch. chenopodioides. Our data confirm
this, although the type species of the latter section, Ch. macro- Within the Atripliceae and the Axyrideae, our analyses reveal
spermum, remains to be included in a molecular analysis. Cheno- two highly supported lineages of Chenopodium sensu lato that have
podium urbicum of section Chenopodia subsection Lejosperma is been recognized at tribal levels (Heklau and Röser, 2008; Kadereit
also part of this clade (Aellen and Just, 1943). This means that et al., 2010; clades 1 and 6, respectively). The Axyrideae might be
smooth or nearly smooth seeds and an indistinctly ridged or sister to all remaining Chenopodioideae (Fig. 1; chloroplast data),
slightly pitted testa must have evolved twice, once in Ch. urbicum also found by Kadereit et al. (2010), or constitute a third branch
and second in the ancestor of the remaining, largely North Amer- (ITS data; Fig. 2). As indicated before, additional nuclear data are
ican species of subsect. Lejosperma, which thus is clearly needed to test this hypothesis. The Atripliceae are congruently in-
polyphyletic. ferred to be nested within Chenopodium sensu lato. Looking at a re-
As currently depicted, the Chenopodium rubrum clade comprises fined tribal classification within Chenopodioideae, they are also
annual herbs with triangular, narrowly triangular, rhombic or lan- nested within Chenopodieae.
ceolate leaf blades, and sinuate, dentate or serrate leaf margins. The Atripliceae clade including Microgynoecium receives high
The inflorescences are composed of subglobose glomerules. The support (97% JK/ 1 PP) based on trnL-F sequence data. The position
flowers have 3–5 tepals, and uniseriate trichomes are only found of Microgynoecium tibeticum as sister to all remaining taxa of Atrip-
on axillary (flower or leaf) buds. The seeds have a rounded margin liceae (96% JK/1 PP trnL-F; Fig. 1) is also depicted here. This is con-
and are smooth or rugulate. gruent to the atpB-rbcL topology in Kadereit et al. (2010), albeit the
The Chenopodium murale clade (Clade 5; 91% JK with trnL-F tree shown in the latter study lacks significant posterior probabil-
and 83% JK with ITS; Fig. 1) contains three species (Ch. murale, ities for the respective nodes. However, our nuclear ITS tree, the
Ch. coronopus and Ch. hybridum), all characterized by rounded, position of Microgynoecium is inconsistently resolved as sister to
compressed and rugose seeds (Iljin, 1936). This feature, not pres- the remaining Atripliceae plus the Chenopodium s.str. clade (50%
ent in all other species sampled so far, seems to be a synapormor- JK/0.83 PP; Fig. 2). The BEAST summary tree based on ITS of Kade-
phy for clade 5. The Chenopodium murale clade is further divided reit et al. (2010) depicts Microgynoecium in yet another position, as
into two well-supported subclades (each 100% JK trnL-F and ITS; sister to the Archiatriplex clade, but again lacking statistical confi-
Figs. 1 and 2): one containing all accessions of Ch. hybridum, dence. The broad scale analysis of Caryophyllales using petD intron
the other all accessions of Ch. murale and Ch. coronopus. Morpho- sequences (Schäferhoff et al., 2009) also indicates a close affinity of
logically, Ch. hybridum differs from the two latter species by hav- Microgynoecium to the Atripliceae, although their taxon sampling of
ing seeds without conspicuously flattened margins (Iljin, 1936). Chenopodiaceae is low. The flowers of Microgynoecium are similar
The Chenopodium murale clade corresponds to the subsection to Archiatriplex (Flores Olvera and Davis, 2001), a fact supporting
Unduata as formally recognized by Mosyakin and Clemants close affinities between these two taxa. Pollen morphology of
(1996). The description of this subsection was based on Ch. mur- Microgynoecium rather stands out from most other taxa of Atripli-
ale as type species (Mosyakin and Clemants, 1996). ceae. Together with Manochlamys, the genus Archiatriplex has very
The large clade shown at the top of Figs. 1 and 2 (clade 7) is large pollen grains but a high pore number with few ektexinous
the clade of Chenopodium s.str., and corresponds to the ‘‘Chen- bodies (Flores Olvera et al., 2006). Overall, our results do not sup-
opodieae I’’ of Kadereit et al. (2003), but excluding Microgynoe- port a relationship between Axyris and Microgynoecium, as sug-
cium. It is sister to the phylogenetically defined Atripliceae gested by Flores Olvera and Davis (2001), based on flower
(Kadereit et al., 2010; clade 6). The position of Microgynoecium morphology. Instead, Microgynoecium most likely belongs to the
was inferred with only weak support as sister to the remaining Atripliceae, although the nuclear-based phylogenies require further
Chenopodieae I using rbcL. There is now increasing evidence that testing through additional genomic regions. Internally, the Atripli-
it rather belongs to the Atripliceae (Fig. 1; see below). The large ceae are composed of two major lineages: one encompassing Atri-
Chenopodium s.str. clade (clade 7) encloses most species of Cheno- plex, the other Grayia brandegeei, G. spinosa and Stutzia dioica (Figs.
podium sampled in this study (>40%), including Chenopodium al- 1 and 2). This corresponds to the Atriplex clade and the Archiatriplex
bum, which is the type species of Chenopodium (Mosyakin and clade in line with the denser sampled analyses of the Atripliceae by
Clemants, 1996), along with the genera Einadia and Rhagodia Kadereit et al. (2010) and Zacharias and Baldwin (2010). Grayia and
(Figs. 1 and 2). Overall, the phylogenetic relationships within this Stutzia share morphological features, such as the presence of car-
core Chenopodium clade are not well resolved. There is also some nose leaves, characteristic inflorescences in glomerules and with
difficulty in finding morphological synapomorphies for the entire non-foliose bracts, and fruits with short bracteoles of less than half
clade. Nevertheless, some characters seem diagnostic to particular the length of the leaves (Flores Olvera and Davis, 2001; Flores Olve-
subclades. Chenopodium vulvaria is characterized by a particular ra et al., 2006; Kadereit et al., 2010).
fetid odour due to its trimethylamine compounds (Croemwell, The Axyrideae appear as an isolated lineage and include Axyris,
1950). It forms an isolated lineage (100% JK/1 PP) in both the Ceratocarpus, and Krascheninnikovia. The genera Ceratocarpus and
ITS and trnL-F trees. Einadia and Rhagodia, which differ from Che- Krascheninnikovia are characterized by the presence of sub-stellate
nopodium by their perennial habit and fleshy fruits (Wilson, dendroid hairs and form a strongly supported subclade, which is
1983), form a well-supported lineage in the trnL-F tree, which sister to Axyris (trnL-F 100% JK/1 PP; ITS 74% JK/0.86 PP), the latter
also includes the Australian Ch. desertorum (92% JK/1 PP). The having sub-stellate branched hairs (Kühn, 1993; Flores Olvera and
chloroplast tree (Fig. 1) further depicts three major subclades, Davis, 2001; Welsh et al., 2003; Zhu et al., 2003; Heklau and Röser,
one comprising the polyploid Ch. album and relatives (the ‘‘Ch. al- 2008). Their close relationship was also suggested based on pollen
bum complex’’), then a lineage of South American diploid species morphology because these three genera share the highest density
(Ch. atrovirens, Ch. pallidicaule and Ch. petiolare), and the biggest of microspines (Flores Olvera et al., 2006). Our results support
one with the allotetraploid Ch. quinoa, and Ch. berlandieri together the monophyly and relationships of Axyris, Ceratocarpus, and
Krascheninnikovia as reported by Heklau and Röser (2008) and nopodium sensu stricto (clade 7) that also contains the type species
Kadereit et al. (2010). However, considering the branching se- of the genus, Ch. album L. (lectotypified by Mosyakin and Clemants,
quence of major clades of the Chenopodioideae, which are all rec- 1996). As a consequence of this study, Einadia Raf. and Rhagodia R.
ognized at tribal level, the subtribe Axyridinae should also be Br. should be included in Chenopodium L. (the necessary new
classified as an own tribe as suggested by Kadereit et al. (2010). names are provided below). The subtribe Rhagodiinae, proposed
by Scott (1978b) to subdivide the Chenopodieae, can therefore not
4.5. Chromosome evolution in Chenopodioideae be upheld. Its diagnostic features, such as a succulent pericarp
and predominantly unisexual flowers (Scott, 1978b), now rather
Differences in chromosome numbers have long been known in appear as homoplastic derived states that arose independently in
Chenopodium and relatives, but so far no attempt has been made to several lineages of the subfamily Chenopodioideae. Holmbergia,
study chromosome evolution in a phylogenetic context (Appendix which was also included in Rhagodiinae by Scott (1978b) based
C). In addition to genome duplications that result in higher ploidy le- on its spongy and inflated berries, was shown to belong to the
vel, as reported from Atriplex (Kühn, 1993; Welsh et al., 2003) and Archiatriplex clade of Atripliceae by Kadereit et al. (2010) and Zach-
Chenopodium s.str. (this study), dysploid changes in chromosome arias and Baldwin (2010).
number were anticipated (Aellen and Just, 1943). The base chromo- Within Chenopodioideae, two additional major clades deserve
some numbers in angiosperms can either correlate with lineages recognition at tribal level. One are the Dysphanieae (Fig. 2). Based
(Schneeweiss et al., 2004; Hidalgo et al., 2007; Blöch et al., 2009) on molecular markers and morphological characters (trichomes),
or evolve independently (e.g., Baldwin and Wessa, 2000; Ellison the monophyly and isolated position of Dysphania, Suckleya, and
et al., 2006). Chenopodioideae provide another case for lineage spe- Teloxys is evident (Clade 2, Figs. 1 and 2). This tribe Dysphanieae
cific dysploid chromosome number changes, as suggested by our re- was already proposed by Pax (1889) but to accommodate the
sults. Whereas a base number of x = 9 can be unambiguously three Australian species of Dysphania within Caryophyllaceae–
inferred for Chenopodioideae, thus corroborating earlier ideas of Alsinoideae. Pax thereby had followed the view of Bentham
Turner (1994), our tree topology suggests independent dysploid (1870) who placed Dysphania rather as an isolated genus in
chromosome loss in two derived lineages. One is found in the subc- Chenopodiaceae than a somewhat abnormal genus of Illecebra-
lade of Ch. ambrosioides, Ch. multifidum and Ch. graveolens (x = 8; ceae (based on Illecebrum, a member of Caryophyllaceae–Alsinoi-
IPCN 1986–2003; Fig. 1). Also, the Spinacia subclade is characterized deae–Paronychieae; Pax, 1889). Almost half a century later, Pax
by the unusual chromosome number of x = 6, that only can be ex- (1927) created an own family Dysphaniaceae for the genus Dys-
plained by a reduction from x = 9 (Fig. 1). Polyploidy, on the other phania, which was based on the valvate perianth and pedicelled
hand, seems to be less characteristic for lineages. It rather seems perianth parts. He considered Dysphaniaceae to be intermediate
to occur within some lineages, such as the Atripliceae and Chenopo- between Chenopodiaceae and Caryophyllaceae, a view upheld in
dium s.str. (clade 7), where speciation may be triggered by polyploid the second edition of the Natürlichen Pflanzenfamilien (Pax and
formation. For Chenopodium, further analysis of clade 7 will be Hoffmann, 1934). Aellen (1960) included Dysphania in Chenopo-
needed to unravel putative events of reticulation and allopolyploid dium as an own section. Eckardt (1967) corroborated this view
speciation. Additional chloroplast markers are necessary to improve by his comparative anatomical study, in which he found the floral
tree resolution and sequences of low copy nuclear genes are needed architecture and gynoecium of Dysphania to strongly differ from
for testing the ITS topology. Illecebraceae. Scott (1978a), however, classified an own subg.
Ambrosia of Chenopodium, based on Ch. ambrosioides as type spe-
4.6. Towards a new tribal and generic classification of cies, but on the other hand kept Dysphania as a separate genus. As
Chenopodioideae indicated above, our phylogenetic data finally show that all the
aromatic species that were shuffled in these pre-cladistic classifi-
Our results support the subdivision of Chenopodium into five cation systems, in fact belong to a single clade that is best named
separate, well-supported clades (Figs. 1 and 2) within Chenopodioi- Dysphania. On a higher level, Dyphania, Suckleya and Teloxis com-
deae. These clades themselves are paraphyletic to other genera. The pose the Dysphanieae. In line with this, and recent molecular find-
necessary taxonomic changes should be oriented at a compromise ings by Kadereit et al. (2010), our results also support the
to conserve traditional use of generic names and to implement inclusion of the subtribe Suckleyinae in Dysphanieae and not in
new molecular results that allow classifying only monophyletic Chenopodieae as originally proposed by Chu et al. (1991).
groups. Keeping a large genus Chenopodium (Aellen and Just, The other lineage that should be recognized at tribal level are
1943; Aellen, 1960; Kühn, 1993; Judd and Ferguson, 1999; Welsh the Spinacieae (clade 3). The tribe Spinacieae was originally de-
et al., 2003) would dramatically underestimate the morphological scribed by Moquin-Tandon (1840) and included Atriplex along with
diversity in this group. It would also result in the inclusion of a number of further genera. The earlier published Atripliceae
well-known genera, such as Atriplex or Spinacia, in Chenopodium. (Meyer, 1829) were then used by most other authors in a circum-
Giving a new name for each clade found by molecular data without scription that included Spinacia.
any other evidence, would add to the current taxonomic confusion In this study, we newly define Spinaceae as different from Atripli-
in the group. ceae and to include the genera Monolepis and Spinacia, along with a
In this study, we found that the highly paraphyletic genus group of Chenopodium species related to Chenopodium capitatum
Chenopodium comprises five lineages which could be recognized and Ch. foliosum (Figs. 1,2) and Scleroblitum (not sampled here but
at generic level (corresponding to clades 2, 3, 4, 5 and 7; Fig. 2). closely related to Ch. foliosum based on rbcL; Kadereit et al., 2003).
However, the situation is complex and further work, including a However, relationships within Spinacieae require further study. An
larger taxon sampling, are needed before the genus can finally be issue will be to test, by inclusion of more taxa and sequence charac-
re-classified. For some clades, the situation is clearer. e.g. Dyspha- ters, if the respective Chenopodium species within this larger clade
nia should be accepted as a genus for the most diverse sublineage are monophyletic. Such a monophyletic assemblage would then cor-
of clade 2 (see Figs. 1 and 2), following the suggestion of Kadereit respond to the Linnaean genus Blitum (Blitum capitatum = Ch. capit-
et al. (2010). The same applies to the genus Teloxys (see above) atum; lectotypified by Mosyakin and Clemants, 1996).
which so far is only sometimes accepted in more recent treat- Even with these realignments, the tribe Chenopodieae remains
ments. All names for the respective genera are already available. paraphyletic to the Atripliceae. Right now, our trees depict two clades
Another clear situation exists for the well supported clade of Che- which are composed of Chenopodium rubrum and relatives (clade 4,
Figs. 1 and 2), and of Chenopodium murale and relatives (clade 5; Figs. Basionym: Einadia trigonos subsp. leiocarpa Paul G. Wilson,
1 and 2), with unclear relationships to each other. Further charac- Nuytsia 4(2): 209. 1983.
ters, both molecular and morphological, are needed to resolve this (3) Chenopodium hastata (R. Br.) S. Fuentes & Borsch, comb.
part of the Chenopodieae and to move towards a stable generic clas- nov.
sification. Finally, phylogenetic classification will either require Basionym: Rhagodia hastata R. Br., Prodr. Fl. Nov. Holland.
establishing one or two additional tribes or merging Atripliceae 408. 1810. Einadia hastata (R. Br.) A.J. Scott, Feddes
and Chenopodieae. Repert. 89: 4 (1978).
In summary, our study showed that the current delimitations of (4) Infraspecific taxa of Chenopodium baccatum Labill.
Chenopodium need to be redefined. We suggest, based on our phy- (4a) Chenopodium baccatum subsp. dioicum (Nees) S. Fuentes
logenetic reconstruction, that the clade 7 (Figs. 1 and 2) may best & Borsch, comb. nov.
represent the monophyletic Chenopodium s.str. Basionym: Rhagodia baccata subsp. dioica (Nees) Paul G.
Wilson, Nuytsia 4(2): 225. 1983. Rhagodia dioica Nees,
5. Taxonomic conclusions Pl. Preiss. 1: 636. 1845.
(5) Chenopodium candolleanum (Moq.) S. Fuentes & Borsch,
For several species of the genera Einadia and Rhagodia, no names comb. nov.
under Chenopodium exist. These are validated in the following treat- Basionym: Rhagodia candolleana Moq., Chenop. Monogr.
ment. However, names under Chenopodium do already exist for a Enum. 10. 1840. Rhagodia baccata var. candolleana
number of species that so far have been treated under Einadia and (Moq.) Moq., Prod. (DC.) 13(2): 50 (1849).
Rhagodia (Wilson, 1983). These are: Chenopodium allanii Aellen; (5a) Chenopodium candolleanum (Moq.) S. Fuentes & Borsch,
Chenopodium baccatum Labill.; Chenopodium polygonoides (Murr.) subsp. candolleanum.
Aellen; Chenopodium preissii (Moq.) Diels; Chenopodium triandrum (5b) Chenopodium candolleanum subsp. argenteum (Paul G.
G. Forster; Chenopodium trigonon Roem. et Schult.; Chenopodium Wilson) S. Fuentes & Borsch, comb. nov.
ulicinum Gand. Basionym: Rhagodia candolleana subsp. argentea Paul G.
Wilson, Nuytsia 4(2): 215. 1983.
(1) Chenopodium nutans (R. Br.) S. Fuentes & Borsch, comb. (6) Chenopodium crassifolium (R. Br.) S. Fuentes & Borsch,
nov. comb. nov.
Basionym: Rhagodia nutans R. Br., Prodr. Fl. Nov. Holland. Basionym: Rhagodia crassifolia R. Br., Prodr. Fl. Nov.
408. 1810. Holland.: 408. 1810.
Einadia nutans (R. Br.) A. J. Scott, Feddes Repert. 89: 3. (7) Chenopodium acicularis (Paul G. Wilson) S. Fuentes &
1978. Borsch, comb. nov.
(1a) Chenopodium nutans (R. Br.) S. Fuentes & Borsch subsp. Basionym: Rhagodia acicularis Paul G. Wilson, Nuytsia
nutans. 4(1): 51. 1982.
(1b) Chenopodium nutans subsp. oxycarpa (Gauba) S. Fuentes (8) Infraspecific taxa of Chenopodium preissii (Moq.) Diels.
& Borsch, comb. nov. (8a) Chenopodium preissii subsp. obovatum (Moq.) S. Fuentes
Basionym: Einadia nutans subsp. oxycarpa (Gauba) Paul G. & Borsch, comb. nov.
Wilson, Nuytsia 4(2): 203. 1983. Basionym: Rhagodia preisii subsp. obovata (Moq.) Paul G.
Rhagodia nutans var. oxycarpa Gauba, Vict. Nat. 65: 167. Wilson, Nuytsia 4(2): 222. 1983. Rhagodia obovata Moq.,
1948. Chenop. Monogr. Enum.: 10 (1840).
(1c) Chenopodium nutans subsp. linifolia (R. Br.) S. Fuentes & (9) Chenopodium latifolium (Benth.) S. Fuentes & Borsch,
Borsch, comb. nov. comb. nov.
Basionym: Einadia nutans subsp. linifolia (R. Br.) Paul G. Basionym: Rhagodia latifolia (Benth.) Paul G. Wilson,
Wilson, Nuytsia 4(2): 204. 1983. Nuytsia 4(2): 228. 1983. Rhagodia crassifolia var. latifolia
Rhagodia linifolia R. Br., Prodr. Fl. Nov. Holland. 408. Benth., Fl. Austral. 5: 155. 1870.
1810. Einadia linifolia (R. Br.) Raf. Fl. Tellur. 4: 121. 1838; (9a) Chenopodium latifolium subsp. rectum (Paul G. Wilson) S.
Ulbrich in Engler et Pratl. Nat. Pflanzenfam. ed. 2, 16c: Fuentes & Borsch, comb. nov.
558. 1934 pro. syn. sub Suaeda linifolia Pall. Einadia Basionym: Rhagodia latifolia subsp. recta Paul G. Wilson,
nutans var. linifolia (R. Br.) A. J. Scott, Feddes Repert. 89: 4. Nuytsia 4(2): 228. 1983.
1978. (10) Chenopodium drummondii (Moq.) S. Fuentes & Borsch,
(1d) Chenopodium nutans subsp. eremaea (Paul G. Wilson) S. comb. nov.
Fuentes & Borsch, comb. nov. Basionym: Rhagodia drummondii Moq., Prod. (DC.) 13(2):
Basionym: Einadia nutans subsp. eremaea Paul G. Wilson, 52. 1849.
Nuytsia 4: 204. 1983. (11) Chenopodium spinescens (R. Br.) S. Fuentes & Borsch,
(2) Infraspecific taxa of Chenopodium trigonon Roem. et comb. nov.
Schult., Syst. Veg. 6: 275. 1820. Basionym: Rhagodia spinescens R. Br., Prodr. Fl. Nov.
(2a) Chenopodium trigonon subsp. stellulatum (Benth.) S. Holland.: 408. 1810.
Fuentes & Borsch, comb. nov. (12) Chenopodium eremaea (Paul G. Wilson) S. Fuentes &
Basionym: Einadia trigonos subsp. stellulata (Benth.) Paul Borsch, comb. nov.
G. Wilson, Nuytsia 4(2): 208. 1983. Chenopodium Basionym: Rhagodia eremaea Paul G. Wilson, Nuytsia 4(2):
triangulare var. stellulatum Benth. Fl. Austral. 5: 161.1870. 232. 1983.
Ch. stellulatum (Benth.) Aellen, Verh. Naturf. Ges. Basel (13) Chenopodium parabolicum (R. Br.) S. Fuentes & Borsch,
41: 93. 1931. nom. illeg., nonAellen, 1928. comb. nov.
(2b) Chenopodium trigonon subsp. leiocarpa (Paul G. Wilson) Basionym: Rhagodia parabolica R. Br., Prodr. Fl. Nov.
S. Fuentes & Borsch, comb. nov. Holland.: 408. 1810.
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This study was carried out in partial fulfilment of a PhD disserta- Bauhinia 3, 327–344.
tion by the first author. Financial support by DAAD (Deutscher Aka- Ellis, J.R., Janick, J., 1960. The chromosomes of Spinacia oleracea. Amer. J. Bot. 47,
210–214.
demischer Austausch Dienst) through a scholarship to S.F. made this
Ellison, N.W., Liston, A., Steiner, J.J., Williams, W.M., Tayler, N.L., 2006. Molecular
work possible. The support of Dr. Monica Moraes and Dr. Stephan phylogenetics of the clover genus (Trifolium-Leguminoseae). Mol. Phylogenet.
Beck as the current and previous directors of the Herbario Nacional Evol. 39, 688–705.
Farris, J.S., Källersjö, M., Kluge, A.G., Bult, C., 1994. Testing significance of
de Bolivia (La Paz) is highly appreciated. We thank the Dirección
incongruence. Cladistics 10, 315–319.
General de Biodiversidad, La Paz, for approving research and collect- Flores Olvera, H., Davis, J.I., 2001. A cladistic analysis of Atripliceae (Chenopodiaceae)
ing permits in Bolivia. We further are especially thankful to Dr. Jim based on morphological data. J. Torrey Bot. Soc. 128, 297–319.
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Molecular Phylogenetics and Evolution 62 (2012) 359–374

Contents lists available at SciVerse ScienceDirect

Molecular Phylogenetics and Evolution

Towards a species level tree of the globally diverse genus

S. Fuentes-Bazan et al. / Molecular Phylogenetics and Evolution 62 (2012) 359–374

Taxon Field/Garden origin Voucher Code trnL-F Acc. ITS Acc.

sect. Orthosporum R. Br.

(continued on next page)

Taxon Field/Garden origin Voucher Code trnL-F Acc. ITS Acc.

Taxon Field/Garden origin Voucher Code trnL-F Acc. ITS Acc.

Tribe Spinaceae Moq. (this study)

Subfamily Camphorosmoideae Luerss.

(continued on next page)

Taxon Field/Garden origin Voucher Code trnL-F Acc. ITS Acc.

Acknowledgments Croemwell, B.T., 1950. The micro-estimation and origin of trimethylamine in

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