Phylogenetic study and taxonomic revision of the Xanthoparmelia mexicana group, including the description of a new species (Parmeliaceae, Ascomycota)
expand article infoAlejandrina Barcenas-Peña, Steven D. Leavitt§, Jen-Pan Huang, Felix Grewe, H. Thorsten Lumbsch
‡ The Field Museum, Chicago, United States of America
§ Brigham Young University, Provo, United States of America
Open Access


Xanthoparmelia (Parmeliaceae, Ascomycota) is the most species-rich genus of lichen-forming fungi. Species boundaries are based on morphological and chemical features, varying reproductive strategies and, more recently, molecular sequence data. The isidiate Xanthoparmelia mexicana group is common in arid regions of North and Central America and includes a range of morphological variation and variable secondary metabolites – salazinic or stictic acids mainly. In order to better understand the evolutionary history of this group and potential taxonomic implications, a molecular phylogeny representing 58 ingroup samples was reconstructed using four loci, including ITS, mtSSU, nuLSU rDNA and MCM7. Results indicate the existence of multiple, distinct lineages phenotypically agreeing with X. mexicana. One of these isidiate, salazinic acid-containing lineages is described here as a new species, X. pedregalensis sp. nov., including populations from xerophytic scrub vegetation in Pedregal de San Angel, Mexico City. X. mexicana s. str. is less isidiate than X. pedregalensis and has salazinic and consalazinic acid, occasionally with norstictic acid; whereas X. pedregalensis contains salazinic and norstictic acids and an unknown substance. Samples from the Old World, morphologically agreeing with X. mexicana, are only distantly related to X. mexicana s. str. Our results indicate that X. mexicana is likely less common than previously assumed and ongoing taxonomic revisions are required for isidiate Xanthoparmelia species.


Cryptic species, lichenised fungi, Mexico, phylogeny, taxonomy


The family Parmeliaceae is the largest family of lichenised fungi (Jaklitsch et al. 2016) currently classified in approximately 70 genera with almost 2,800 species (Lumbsch and Huhndorf 2010, Divakar et al. 2017). Xanthoparmelia, with about 800 described species, is the largest genus of lichen-forming fungi (Lücking et al. 2016), with two centres of distribution in Australia and southern Africa; a smaller number of species occur in the Holarctic (Blanco et al. 2004, Eriksson et al. 2004, Crespo et al. 2010, Thell et al. 2012, Leavitt et al. 2018). To date, 74 species have been reported from Mexico, amongst these species, 27 are isidiate (Nash et al. 2016).

Isidiate Xanthoparmelia species are distributed in boreal, temperate and tropical regions. However, they commonly occur in semi-arid to arid regions worldwide especially on siliceous rocks, such as granite and sandstone. In North and Central America, Xanthoparmelia mexicana (Gyelnik) Hale ranks amongst the most common isidiate species. This taxon is widely distributed and has been reported from western USA, Mexico, Dominican Republic, Argentina, Kenya, Australia, New Zealand, Japan, China and Nepal (Hale 1990, Elix 1994, Nash and Elix 2004). X. mexicana is part of a complex of morphologically similar species, with adnate to slightly attached thalli, cylindrical isidia and a brown lower side of the thalli, which are primarily separated by their secondary metabolites. The species complex also includes X. ajoensis (T. H. Nash) Egan (diffractaic acid), X. dierythra (Hale) Hale (norstictic acid), X. joranadia (T. H. Nash) Hale (lecanoric acid), X. maricopensis T. H. Nash & Elix (norstictic and hyposalazinic acids), X. moctezumensis T. H. Nash (3-α-hydroxybarbatic acid), X. plittii (Gyelnik) Hale (stictic acid), X. schmidtii Hale (barbatic, norstictic and salazinic acids), X. subramigera (Gyelnik) Hale (fumarprotocetraric acid) and X. weberi (Hale) Hale (hypoprotocetraric acid) (Hale 1990, Nash et al. 2016). However, previous studies indicate that current interpretations of morphological features and secondary metabolites likely fail to accurately characterise species-level diversity in isidiate Xanthoparmelia species (Leavitt et al. 2011, 2013).

To better understand the evolutionary history of the Xanthoparmelia mexicana complex and potential taxonomic implications, isidiate Xanthoparmelia specimens were collected from different locations throughout arid regions of Mexico and supplemented with previously available sequence data. The new samples came from xerophytic scrublands in the states Puebla, Oaxaca, San Luis Potosí, Querétaro, Estado de México, Mexico City, Guanajuato, Zacatecas and Hidalgo, all in the central part of Mexico. We focused on sampling Xanthoparmelia populations that were phenotypically similar to X. mexicana, e.g. isidiate specimens containing salazinic acid. X. mexicana was originally described by Gyelnik (1931) as Parmelia mexicana and was later combined into Xanthoparmelia by Hale (1974). The type specimen was collected from San Jerónimo, in Pedregal de San Angel, Mexico City. The syntype in the Bouly de Lesdain herbarium was destroyed during World War II, whereas the lectotype in the Budapest herbarium (BP) was not available for molecular study. Therefore, we attempted to recollect material at the type locality of X. mexicana and other regions throughout Mexico. Based on the results of this study, we formally describe a previously unrecognised species-level lineage comprised of isidiate specimens as new to science.

Material and methods

Taxon sampling

Specimens were studied from the herbaria ASU, BRY, F, MAF and new collections from different localities throughout arid regions from the central part of Mexico (Table 1, Fig. 1). A total of 83 specimens, representing 43 species were included, with an emphasis on isidiate species/populations from Central and North America (all epithets are validly published, with the exception of X. isidiomontana nom prov assigned to the clade ‘D2’ from Leavitt et al. 2013). New sequences were generated from 25 specimens and supplemented with 34 sequences from a previous analysis (Leavitt et al. 2018) and 24 additional sequences from GenBank (Table 1). Four species in the genus Xanthoparmelia that have previously been shown to be distantly related to X. mexicana were used as outgroup – X. beatricea, X. austroafricana, X. subramigera and X. aff. subramigera (Leavitt et al. 2018).

Collection information for specimens included in the present study: Species, morphological/chemical species identification; DNA code, individual code associated with specimen label in multiple sequence alignments; Species distribution; Voucher information; and GenBank accession numbers for sampled loci in bold text indicates new sequences generated for this study. Specimens sequenced using Illumina technology are indicated by a • with the associated DNA code.

Species DNA code Voucher ITS MCM7 mtSSU nuLSU
X. aff. chlorochroa 082f USA: Utah; Leavitt et al. 55225 (BRY-C) MG695498 MG695699 MG695746 MG695599
X. aff. chlorochroa 9866 USA: Nevada; Leavitt & St. Clair 9866 (BRY-C) MG695499 MG695700 MG695747 MG695600
X. aff. coloradoensis 135f USA: Utah; Leavitt et al. 55255 (BRY-C) MG695500 MG695701 MG695748 MG695601
X. aff. protomatrae GenBank Spain: Zamora; Blanco & Crespo 6216 (MAF-Lich) AY581104 AY582339 AY578972
X. aff. subramigera 9664 Kenya: Coast, Kirika & Lumbsch 4117 (F) MG695515 MG695764 MG695616
X. ajoensis 14908 Mexico: Puebla; Barcenas-Peña 5898 (F) MH580218 MH686124 MH699893 MH699913
X. ajoensis 14920 Mexico: Puebla; Barcenas-Peña 5900 (F) MH580219 MH686125 MH699894 MH699914
X. ajoensis 14934 Mexico: Puebla; Barcenas-Peña 5914 (F) MH580220 MH580220 MH699895 MH699915
X. angustiphylla GenBank USA: Blanco et al. 6768 (MAF) AY581092 AY582328
X. atticoides GenBank USA: Blanco et al. 6744 (MAF) AY581066 AY582302 AY578929
X. austroafricana 9549 Kenya: Coast Prov., Kirika 4485 (F) MG695542 MG695644
X. beatricea E467 Kenya: E467 (MAF-Lich 17174) JQ912367 MG695793 JQ912462
X. camtschadalis 1 GenBank USA: Leavitt et al. 55174 (BRY-C) HM578630 HM579042
X. camtschadalis 2 GenBank USA: Leavitt et al. 55291 (BRY-C) HM578744 HM579156
X. cf. mexicana 016m Pakistan: Tattu; Kahlid, Usman & Khan MKF16 (LAH) MH580221
X. cf. mexicana 016m2 Pakistan: Swat Valley; Khan & Khalid SW-16 (LAH) MH580222
X. chlorochroa 536f USA: North Dakota; G. Lind 1213 (BRY-C) HM578887 HM579688 KR995372 HM579298
X. conspersa GenBank Spain: Zamora, Blanco & Crespo s.n. (MAF-Lich 6793) AY581096 AF351186 AY578962
X. cordillerana E422 Chile: E422 (MAF-Lich 17198) JQ912358 MG695797 JQ912453
X. coreana 1 GenBank South Korea: Hur, J.-S. 005561 KJ170890 KJ170890
X. coreana 2 GenBank South Korea: Hur, J.-S. 005589 KJ170883 KJ170883
X. coreana 3 GenBank South Korea: Hur, J.-S. 013905 KJ170873 KJ170873
X. cumberlandia nybg02 USA: Maine; R. Harris 55563 (NY) MG695545 MG695798 MG695646
X. dierythra 226f USA: Leavitt et al. 55300 (BRY-C) HM578753 HM579569 HM579165
X. dierythra 439f USA: Leavitt et al. 55383 (BRY-C) HM578833 HM579245
X. dierythra 098f Mexico: Puebla; Leavitt et al. 55234 (BRY-C) HM578689 HM579504 HM579099
X. hirolsakiensis GenBank South Korea: Hur, J.-S. 010532 KJ170876 KJ170876
X. hypofusca 8837 USA: West Virginia; Streets (02086946 NY) MG695550 MG695717 MG695803 MG695651
X. idahoensis 1 GenBank USA: Leavitt et al. 55463 (BRY-C) HM578915 HM579708 HM579323
X. idahoensis 2 GenBank USA: Leavitt et al. 55354 (BRY-C) HM578805 HM579620 HM579216
X. infrapallida 9904 USA: Arizona; Leavitt 9904 (BRY-C) MG695555 MG695720 MG695809 MG695656
X. isidiovagans GenBank Spain: 9956 (MAF-Lich) AY581094 JX974718 AY582330 AY578960
X. lavicola GenBank USA: Leavitt et al. 55230 (BRY-C) HM578685 HM579500
X. lavicola 15489 Mexico: Morelos; Nash III 46261 (WIS) MH580227 MH686131 MH699920
X. lavicola 14894 Mexico: Puebla; Barcenas-Peña 5857 (F) MH580223 MH686127 MH699896 MH699916
X. lavicola 14905 Mexico: Puebla; Barcenas-Peña 5884 (F) MH580224 MH686128 MH699897 MH699917
X. lavicola 14906 Mexico: Oaxaca; Barcenas-Peña 5905 (F) MH580225 MH686129 MH699898 MH699918
X. lavicola 14910 Mexico: Puebla; Barcenas-Peña 5888 (F) MH580226 MH686130 MH699899 MH699919
X. lineola 245f USA: Arizona; EA collection 31–259 (55306 BRY-C) MG695556 MG695721 MG695810 MG695657
X. maricopensis 6698 USA: Arizona; J. Leavitt 001 (BRY-C) MG695558 MG695723 MG695812 MG695659
X. mexicana 291f USA: Leavitt et al. 55328 (BRY-C) HM578780 HM579596 HM579192
X. mexicana 786f USA: Leavitt et al. 55462 (BRY-C) HM578914 HM579707 HM579322
X. mexicana 097f Mexico: Leavitt et al. 55233 (BRY-C) HM578688 HM579503 - HM579098
X. mexicana GenBank South Korea: Jang et al. 005486 (KoLRI) KM250123
X. mexicana 15479 Mexico: San Luis Potosí; Barcenas-Peña 7316 (F) MH580231 MH686135 MH699904 MH699923
X. mexicana 15472 Mexico: San Luis Potosí; Barcenas-Peña 7408 (F) MH580229 MH699932 MH699922
X. mexicana 15466 Mexico: San Luis Potosí; Barcenas-Peña 7441 (F) MH686404 MH686133 MH699902
X. mexicana 15461 Mexico: Querétaro; Barcenas-Peña 7178 (F) MH686401 MH699930 MH699901
X. mexicana 15485 Mexico: Querétaro; Barcenas-Peña 7209 (MEXU) MH686402 MH686136 MH699905
X. mexicana 15471 Mexico: San Luis Potosí; Barcenas-Peña 7273 (F) MH686403 MH699931 MH699903
X. mexicana 15473 Mexico: Hidalgo; Nash III 45126 (WIS) MH580230 MH686134
X. mexicana 156f USA: Leavitt et al. 55267 (BRY-C) HM578721 HM579536 HM579132
X. mexicana 15487 Mexico: Hidalgo; Barcenas-Peña 7470 (F) MH580232 MH686137 MH699906
X. mexicana 14899 Mexico: Oaxaca; Barcenas-Peña 5918 (F) MH580228 MH686132 MH699900 MH699921
X. moctezumensis 14897 Mexico: Puebla; Barcenas-Peña 5891(F) MH580233 MH686138 MH699907 MH699924
X. norchlorochoroa 1 GenBank USA: Leavitt et al. 55157 (BRY-C) HM578613 HM579432 HM579025
X. norchlorochoroa 2 GenBank USA: Leavitt et al. 55447 (BRY-C) HM578899 HM579693 HM579307
X. orientalis GenBank South Korea: Hur, J.-S. 005613 KJ170884 KJ170884
X. pedregalensis 527 Mexico: Mexico City; Ruiz-Cazares 1552 (F) MH580238 MH707353 MH699912 MH699929
X. pedregalensis 526 Mexico: Mexico City; Ruiz-Cazares 1553 (MEXU) MH580234 MH707352 MH699908 MH699925
X. pedregalensis 533 Mexico: Mexico City; Ruiz-Cazares 1557 (F) MH580236 MH699910 MH699927
X. pedregalensis 529 Mexico: Mexico City; Ruiz-Cazares 1555 (F) MH580235 MH686139 MH699909 MH699926
X. pedregalensis 531 Mexico: Mexico City; Ruiz-Cazares 1559 (MEXU) MH580237 MH707354 MH699911 MH699928
X. plittii 498f USA: North Carolina; Leavitt et al. (55422 BRY-C) MG695562 MG695727 MG695664
X. psoromifera 1 GenBank USA: Leavitt et al. 55314 (BRY-C) HM578766 HM579582 HM579178
X. psoromifera 2 GenBank USA: Leavitt et al. 55313 (BRY-C) HM578765 HM579581 HM579177
X. pulvinaris GenBank Hungary: Molnar et al. 93943 (BP) JQ362484 JQ362485 JQ362486
X. isidiomontana nom. prov. 292f USA: Nevada; Leavitt (55329 BRY-C) MG695579 MG695733 MG695834 MG695679
X. isidiomontana nom. prov. E1010 Spain: E1010 (MAF-Lich 17181) JQ912354 MG695835 JQ912451
X. isidiomontana nom. prov. E984 USA: E984 (MAF-Lich 17199) JQ912386 MG695836 JQ912479
X. stenophylla 5040 Kazakhstan: Karkaralinsk; Tshernyshev (BRY-C) MG695583 MG695737 MG695843 MG695683
X. stenophylla E708 Turkey: E708 (MAF-Lich 17196) JQ912372 MG695844 JQ912467
X. subcumberlandia 121f USA: Utah; Leavitt et al. (55242 BRY-C) MG695584 MG695738 MG695845 MG695684
X. subdifluens 1 GenBank Spain: de Paz et al. 17178 (MAF-Lich) JQ912381 JQ912474
X. subdifluens 2 GenBank Spain: Blanco et al. 9910 (MAF) AY581105 AY582340 AY578973
X. sublaevis GenBank Spain: Tenerife, Canary Islands; Blanco et al. 7460 (MAF) AY581106 AY582341 AY578974
X. subramigera 9668 Kenya: Coast, Kirika 4583 (F) MG695525 MG695709 MG695774 MG695626
X. tuberculiformis GenBank South Korea: Jang et al. 012058 (KoLRI) KM250131 KM250131
X. vicentei GenBank Spain: Salamanca; Crespo & Molina (7248 MAF-Lich) AY581112 AY582347 AY578980
X. viriduloumbrina1 GenBank USA: Pennsylvania; Lendemer 13314: 1049917 (NY) HM066945
X. viriduloumbrina 2 GenBank USA: Pennsylvania; Lendemer 13325: 1049906 (NY) HM066944
X. wyomingica 001f USA: Utah; Leavitt et al. (55151 BRY-C) MG695598 MG695745 MG695864 MG695698
X. wyomingica 826f USA: Wyoming; Leavitt 826 (55501 BRY-C) HM578953 HM579746 HM579360
Figure 1. 

Location of new Xanthoparmelia recollection sites from arid regions from central part of Mexico. Oaxaca (pink), Puebla (green), Mexico City (red), Estado de México (blue), Querétaro (purple), Guanajuato (brown), Hidalgo (grey), Aguas Calientes (yellow), San Luis Potosí (black), Zacatecas (orange).

Morphology and chemistry

Morphological characters were observed using a Zeiss Stemi 2000-C stereoscope. Ascomatal anatomy, ascospore in addition to conidia shape and size were observed using a Zeiss Axioscope. Secondary metabolites were identified using spot test KOH 10%, KC, C, PD and high-performance thin layer chromatography (HPTLC), using solvent systems C following established methods (Culberson and Johnson 1982, Arup et al. 1993, Lumbsch 2002, Orange et al. 2010).

Molecular methods

Total genomic DNA was extracted from thallus fragments following the manufacturers’ instructions using the ZR Fungal/Bacterial DNA Miniprep Kit (Zymo Research Corp., Irvine, CA). DNA sequences were generated for four markers using polymerase chain reaction (PCR): the nuclear ribosomal internal transcribed spacer region (ITS), a fragment of nuclear large subunit rDNA (nuLSU), the nuclear protein-coding marker minichromosome maintenance complex component 7 (MCM7) and a fragment of the mitochondrial small subunit rDNA (mtSSU). PCR reactions contained 6.25 ml of MyTaq Mix, 25 ml H2O, 0.25 ml forward and reverse primer and 0.5 ml template DNA, for a total reaction volume of 12.5 ml. The ITS region was amplified using primers ITS1F (Gardes and Bruns 1993) and ITS4 (White et al. 1990); MCM7 using primers MCM7-709f and Mcm7-1348r (Schmitt et al. 2009), mtSSU using primers mrSSU1 and mrSSU3R (Zoller et al. 1999) and nuLSU rDNA using primers AL2R (Mangold et al. 2008) and LR6 (Vilgalys and Hester 1990). PCR products were sequenced using an ABI PRISM 3730 DNA Analyser (Applied Biosystems) at the Pritzker Laboratory for Molecular Systematics and Evolution at The Field Museum, Chicago, Illinois, USA. Nine specimens were obtained previously for a global phylogenetic study of the genus and sequenced using next generation sequencing technology as described in Leavitt et al. (2018) (Table 1). In short, metagenomic Nextera libraries (prepared from total DNA extraction) were sequenced on the Nextseq platform at the Core Genomics Facility at the University of Illinois at Chicago, USA. Illumina reads of each specimen were mapped to reference marker sequences downloaded from Genbank (ITS AY581063, nuLSU HM125760, MCM7 HM579689, mtSSU KR995373) using the mapping feature implemented in Geneious v11.0.3 (, Kearse et al. 2012). The consensus sequence of each locus was extracted and added to the data set of Sanger sequences to build a combined alignment.

Sequence alignment and phylogenetic analysis

Sanger sequences, consensus Illumina reads and sequences available on GenBank were added to an alignment published in Leavitt et al. (2018) using Mafft v7 with the option ‘add sequence’ (Table 1). ITS, MCM7, mtSSU and nuLSU sequences were aligned independently using the ‘automatic’ option in Mafft v7, with the remaining parameters set to default values. Ambiguous positions of each one-locus alignment were removed using options for a “less stringent” selection on Gblocks 0.91b (Castresana 2000). SequenceMatrix software (Vaidya et al. 2011) was used for the alignment concatenation. Phylogenetic analyses were performed using Maximum Likelihood (ML) and Bayesian Analysis (BA). ML trees were calculated with RAxML-HPC2 on XSEDE 8.2.10 (Stamatakis 2014) on the Cipres Science Gateway (Miller et al. 2010) using GTR+G+I substitution model with 1000 bootstrap pseudoreplicates. For the BA, substitution models for each locus were estimated using jModelTest-2.1.9 (Guindon and Gascuel 2003, Darriba et al. 2012): in ITS the TIM2ef+I+G, in MCM7 the K80+G, in mtSSU the TPM2uf+I and in nuLSU the TrN+I were used. Two parallel Markov chain Monte Carlo (MCMC) runs were performed in MrBayes 3.2.6 (Huelsenbeck and Ronquist 2001, Ronquist and Huelsenbeck 2003), each using 10,000,000 generations which were sampled every 100 steps. A 50% majority rule consensus tree was generated from the combined sampled trees of both runs after discarding the first 25% as burn-in. Tree files were visualised with FigTree 1.4.2 (Rambaut 2014). The ITS, MCM7, mtSSU and nuLSU sequences are deposited in GenBank (Table 1).

Results and Discussion


Results from phylogenetic analyses presented here clearly indicate that the taxonomy in the Xanthoparmelia mexicana group requires revision because different samples assigned to the same species based on phenotypical characters may not form a monophyletic group. Specimens identified as X. mexicana from Asia (Pakistan and South Korea) were distantly related to samples of the species collected in North America and Europe (included in X. isidiomontana nom prov) (Fig. 2). The latter specimens fell into three distinct and well supported clades (clade I-III in Fig. 2). Note that the three distinct and well supported clades did not form a monophyletic group.

Figure 2. 

Phylogenetic relationships of the Xanthoparmelia mexicana group based on a concatenated data set of ITS, mtSSU, nuLSU and MCM7. Topology based on maximum likelihood (ML) analyses. Bootstrap values above 75 and 0.95 posterior probability are indicated on each branch. The clades I, II and III are highlighted in blue, yellow and pink, respectively. Selected specimens representing clades (habit and isidia): I, X. mexicana s. lat. (A, B); II, X. pedregalensis (C, D) and III, X. mexicana s. str. (E, F), a picture of the X. mexicana type specimen from BP is included (G).

Clade ‘I’ (=X.isidiomontananom prov, ‘D2’ in Leavitt et al. 2013) included isidiate specimens from North America and Europe and samples identified as X. dierythra, X. mexicana (Figs 2A and B) and X. plittii, in addition to a number of non-isidiate, fertile specimens. Additional studies will be necessary to better understand the delimitation of X. dierythra, which is also polyphyletic and is currently accommodating specimens with norstictic acid and lacking salazinic acid (Hale 1990). This clade likely represents another species-level lineage lacking formal taxonomic recognition and a formal description of this lineage will be proposed once the phylogenetic placement of X. dierythra s. str. is ascertained.

Clade ‘II’ included specimens collected in the Pedregal, south of Mexico City, which is also the type locality of X. mexicana. However, the new material does not correspond phenotypically with the type specimen of X. mexicana in BP (Fig. 2G). These specimens are different from X. mexicana specimens (represented by Clade III in phylogenetic analysis) in having less contiguous lobes, densely isidiate thallus, presence of salazinic acid, norstictic acid and an unknown substance. Since clade ‘II’ differs phylogenetically and phenotypically from clade ‘III’ (representing X. mexicana s. str. – see below), we describe clade ‘II’ as a species new to science, X. pedregalensis (Figs 2C and D).

Clade ‘III’ includes the majority of samples identified as X. mexicana collected in different localities of Mexico (Oaxaca, Puebla, San Luis Potosí, Querétaro, Hidalgo). Specimens recovered in this clade were morphologically and chemically similar to the lectotype of X. mexicana in BP (Fig. 2G). Therefore, clade ‘III’ is here recognised as X. mexicana s. str. (Gyelnik 1931, Hale 1974) (Figs 2E and F). So far, we have only been able to confirm the presence of X. mexicana s.str. in Mexico. Specimens collected in other areas and previously identified as X. mexicana likely represent different species. For example, none of the samples from Asia or those reported in Leavitt et al. (2013) from western United States belongs to X. mexicana s. str. Further studies are needed to evaluate the occurrence of this species in other parts of the world, including North America and Europe.

Underestimates of species diversity is common amongst under-studied organismal groups (Pawar 2003, Chiarucci et al. 2011, Lücking 2012, Coleman 2015, Troia and McManamay 2016, Troudet et al. 2017), which is particularly evident in lichenised fungi (Crespo and Perez-Ortega 2009, Crespo and Lumbsch 2010, Leavitt et al. 2011, Lumbsch and Leavitt 2011, Leavitt et al. 2013, Leavitt et al. 2016, Lücking et al. 2016, Leavitt et al. 2018). Previous studies concluded that the species delimitation in lichenised ascomycetes with traditional morphological and chemical characters are apparently misleading with respect to species diversity. In the study of Leavitt et al. (2016), several new taxa were described primarily based on evidence from genetic data, but it does not preclude the possibility that additional studies investigating morphological and chemical characters may identify additional independent characters or combinations of characters, supporting the species circumscribed using molecular data. Our results corroborate findings from the previous studies by showing the need of an integrative approach using not only conventional (i.e. morphology and TLC data), but also new sets of data (e.g. DNA sequence data) to better understand the pattern of species diversity. Our study shows that, by incorporating molecular data, the taxonomic status of a conventionally difficult group based on morphology can be resolved: the three main clades belonging to the X. mexicana complex do not form a monophyletic group based on our newly reconstructed phylogeny (Fig. 1). In this context, the species diversity in the X. mexicana complex is likely under-estimated and morphologically cryptic species may be identified in the future.


Xanthoparmelia pedregalensis Barcenas-Peña, Lumbsch & Leavitt, sp. nov.

MycoBank No: MB826958
Figs 2C and D


MEXICO. Ciudad de México: Coyoacán, Pedregal de San Angel, 19°19'8.3"N, 99°11'25.93"W, 2321 m elev., xerophytic scrub, on rocks, November, 2017, Ruiz Cazares 1553 (MEXU-holotype), same locality and date Ruiz Cazares 1559 (MEXU-paratype).


Thallus moderately adnate to adnate, imbricate, upper surface yellow-green, lower surface tan-brown, abundant isidia subglobose to cylindrical, simple to branched and medulla containing salazinic and norstictic acids as major compounds and an unknown substance. Differing from the phenotypically similar X. mexicana by nucleotide position characters in the ITS sequence as shown in Table 2.

Differences of nucleotide positions in the ITS marker between X. mexicana and X. pedregalensis.

Species Aligned nucleotide position characters in the ITS marker
36 115 379 425 450 466 488 496
X. mexicana G C A C T C/T G A
X. pedregalensis A T G G C A C G


The taxon name is based on its occurrence in the Pedregal de San Angel region of Mexico.


Thallus foliose, moderately adnate to adnate, 2–7 cm in diam., irregularly lobate; lobes subirregular, elongate, plane to subconvex, 1.5–3 mm wide, not lobulate; apices subrotund, smooth, eciliate. Upper surface yellow-green, smooth, shiny, epruinose and emaculate, densely isidiate; isidia initially subglobose, becoming cylindrical to coralloid branched with age, 0.1–0.2 mm in diam., 0.1–0.9 mm tall; tips syncorticate, brown to dark brown, sometimes weakly erumpent; soralia and pustulae absent. Medulla white, with continuous algal layer. Lower surface tan to brown, plane, moderately rhizinate; rhizines pale to dark brown, simple, 0.5–0.9 mm long. Apothecia rare, sessile, 1–2 mm wide, laminal on thallus; disc cinnamon-brown to dark brown; margin smooth, pruina absent; asci: clavate, 8-spored; ascospores hyaline, simple, ellipsoid, 9–10 × 4–5 µm. Pycnidia rare, immersed conidia bifusiform, 5–7 × 1 µm.

Secondary metabolites

Upper cortex K–, C–, KC–, P–; medulla K+ yellow then dark red, KC–, C–, P+ yellow-orange. Upper cortex with usnic acid (major); medulla with salazinic (major) and norstictic acids (submajor) and an unknown substance (minor) (Rf 28–30, brown in daylight after heating, UV brown-dark, yellow halo after heating).

Distribution and ecology

The new species was found in xerophytic scrub vegetation, in Pedregal de San Angel south of Mexico City, growing on volcanic rocks. It is currently known only from the type locality.


Xanthoparmelia pedregalensis is morphological and chemically similar to X. mexicana. However, the latter has more contiguous lobes and is less isidiate than X. pedregalensis. In addition X. mexicana has salazinic (major) and consalazinic acid (minor) and usually norstictic and protocetraric acids (trace) in the medulla, whereas X. pedregalensis contains salazinic (major) and norstictic acids (submajor) and an unknown substance. Distinguishing the two species is supported by molecular data.

Additional specimens examined

Mexico. Ciudad de México: Coyoacán, Pedregal de San Angel, 19°19'8.3"N, 99°11'25.93"W, 2321 m elev., xerophytic scrub, on rocks, November, 2017, Ruiz Cazares 1552 (MEXU); 19°19'15.19"N, 99°11'15.22"W, 2311 m, Ruiz Cazares 1555, 1557 (F).

New state records

Xanthoparmelia ajoensis (Nash) Egan, 1975: 217.

Parmelia ajoensis Nash, 1974: 234. [Type collection: Organ Pipe Cactus National Monument, Pima Co., Arizona, USA, Nash 5999 (ASU, holotype; DUKE, US, isotypes).] New to Oaxaca, X. ajoensis is distributed across western USA and Mexico where it has previously been reported from Baja California Sur, Durango, Morelos, Puebla, Sinaloa and Sonora on acidic rocks, often in open, arid habitats at relatively low elevations (Hale 1990, Nash and Elix 2004, Nash et al. 2016).

Specimens Examined: Mexico. Oaxaca: Quiotepec, 17°54'18.9"N, 96°58'01.8"W, 696 m elev., xerophytic scrub, on rock, October, 2016, Barcenas-Peña 5906, 5908, 5913, 5915 (MEXU).

Xanthoparmelia moctezumensis Nash in C. Culberson, Nash & Johnson, 1979: 155. [Type collection: 28 km E of Moctezuma, Sonora, Mexico, Nash 12548 (ASU, holotype; DUKE, US, isotypes).]

New to Puebla. Xanthoparmelia moctezumensis is distributed throughout south-western USA and Mexico where it has been reported from Baja California Sur, Durango, Sinaloa and Sonora on acidic rocks, often in open, arid to woodland habitats (Nash and Elix 2004, Nash et al. 2016).

Specimens Examined: Mexico. Puebla: San Rafael Coxcatlán, 18°13'16.6"N, 97°07'22.4"W, 1148 m elev., xerophytic scrub, on rock, October, 2016, Barcenas-Peña 5887, 5890, 5891, 5893 (MEXU).

Xanthoparmelia mexicana (Gyelnik) Hale, 1974: 488.

New to Querétaro, San Luis Potosí and Zacatecas. Xanthoparmelia mexicana has been reported from Baja California, Baja California Sur, Chihuahua, Coahuila, Distrito Federal, Durango, Guanajuato, Hidalgo, Jalisco, Michoacán, Nuevo León, Oaxaca, Puebla, Sonora and Veracruz, on acidic rocks, often on soil near the coast in open, arid habitats (Nash et al. 2004, 2016).

Specimens Examined: Mexico: Querétaro. Tequisquiapan, Rancho Las Fuentes, 20°33'51.0"N, 100°01'54.6"W W, 1942 m elev., xerophytic scrub, on rock, August, 2017, Barcenas-Peña 7516; San Luis Potosí, Mexquitic de Carmona, La Campana, 22°15'28.9"N, 101°05'26.8"W, 2012 m elev., xerophytic scrub, on rock, August, 2017, Barcenas-Peña 7441; Zacatecas, Fresnillo, El Poleo, 23°06'16.4"N, 102°54'24.3"W, 2227 m elev., xerophytic scrub, on rock, August, 2017, Barcenas-Peña 7356 (all MEXU).


The first author thanks the National Council of Science and Technology (CONACYT) by grants for supporting her research stay to the Field Museum. We are grateful to Dr. Tom Nash III, Biol. Alin Ruiz and José Vladimir Rodríguez for sending us the specimens. We are grateful to Dr. Armando Burgos and Biol. Maricarmen Altamirano for their assistance in the field work. We are grateful to Dra. Silke Cram for logistical support at Reserva Ecológica del Pedregal de San Angel. The authors are thankful to the Pritzker Laboratory for Molecular Systematics at the Field Museum. We thank to Negaunee Foundation for financial support.


  • Arup U, Ekman S, Lindblom L, Mattsson J-E (1993) High performance thin layer chromatography (HPTLC), an improved technique for screening lichen substances. Lichenologist 25: 61–71.
  • Blanco O, Crespo A, Elix JA, Hawksworth DL, Lumbsch HT (2004) A molecular phylogeny and a new classification of parmelioid lichens containing Xanthoparmelia-type lichenan (Ascomycota: Lecanorales). Taxon 53: 959–975.
  • Chiarucci A, Bacaro G, Scheiner SM (2011) Old and new challenges in using species diversity for assessing biodiversity. Philosophical Transactions of the Royal Society B 366: 2426–2437.
  • Coleman CO (2015) Taxonomy in times of the taxonomic impediment – examples from the community of experts on amphipod crustaceans. Journal of Crustacean Biology: 35: 729–740.
  • Crespo A, Pérez-Ortega S (2009) Cryptic species and species pairs in lichens: A discussion on the relationship between molecular phylogenies and morphological characters. Anales del Jardín Botánico de Madrid 66: 71–81.
  • Crespo A, Kauff F, Divakar PK, Prado RD, Pérez-Ortega S, Amo G, Ferencova Z, Blanco O, Roca-Valiente B, Núñez-Zapata J, Cubas P, Argüello A, Elix JA, Esslinger TL, Hawksworth DL, Millanes A, Molina MC, Wedin M, Ahti T, Aptroot A, Barreno E, Bungartz F, Calvelo S, Candan M, Cole M, Ertz D, Goffinet B, Lindblom L, Lücking R, Lutzoni F, Mattsson JE, Messuti MI, Miadlikowska J, Piercey-Normore M, Rico VJ, Sipman HJM, Schmitt I, Spribille T, Thell A, Thor G, Upreti DK, Lumbsch HT (2010) Phylogenetic generic classification of parmelioid lichens (Parmeliaceae, Ascomycota) based on molecular, morphological and chemical evidence. Taxon 59: 1735–1753.
  • Culberson C, Johnson A (1982) Substitution of methyl tert.-butyl ether for diethyl ether in standardized thin layer chromatographic method for lichen products. Journal of Chromatography B 238: 438–487.
  • Culberson CF, Nash III TH, Johnson A (1979) 3-a-Hydroxybarbatic Acid, a New Depside in Chemosyndromes of Some Xanthoparmeliae with ß-Orcinol Depsides. Bryologist 82: 154–161.
  • Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9(8): 772.
  • Divakar PK, Crespo A, Kraichak E, Leavitt SD, Singh G, Schmitt I, Lumbsch HT (2017) Using a temporal phylogenetic method to harmonize family- and genus-level classification in the largest clade of lichen-forming fungi. Fungal Diversity 84: 101–117.
  • Egan RS (1975) New Xanthoparmelia (Lichenes: Parmeliaceae) Records from New Mexico. Mycotaxon 2: 217–222.
  • Elix JA (1994) Xanthoparmelia. Flora of Australia 55: 201–308.
  • Eriksson OE, Baral HO, Currah RS, Hansen K, Kurtzman CP, Rambold G, Laessøe T (2004) Outline of Ascomycota–2004. Myconet 10: 1–99.
  • Gyelnik V (1931) Additamenta ad cognitionem Parmeliarum II. Fedde Repertorium Specierum Novarum Regni Vegetatis 29: 273–291.
  • Hale ME (1974) Bulbothrix, Parmelina, Relicina and Xanthoparmelia, Four New Genera in the Parmeliaceae (Lichenes). Phytologia 28: 479–490.
  • Hale Jr ME. (1990) A synopsis of the lichen genus Xanthoparmelia (Vainio) Hale (Ascomycotina, Parmeliaceae). Smithsonian Contributions to Botany 74: 1–250.
  • Jaklitsch WM, Baral HO, Lücking R, Lumbsch HT (2016) Ascomycota. In: Frey W (Ed.) Syllabus of Plant Families - Adolf Engler’s Syllabus der Pflanzenfamilien. Gebr. Borntraeger Verlagsbuchhandlung, Stuttgart, 1–150.
  • Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Mentjies P, Drummond A (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28: 1647–1649.
  • Leavitt SD, Johnson LA, Goward T, St. Clair LL (2011) Species delimitation in taxonomically difficult lichen-forming fungi: An example from morphologically and chemically diverse Xanthoparmelia (Parmeliaceae) in North America. Molecular Phylogenetics and Evolution 60: 317–332.
  • Leavitt SD, Lumbsch HT, Stenroos S, Clair LL (2013) Pleistocene Speciation in North American Lichenized Fungi and the Impact of Alternative Species Circumscriptions and Rates of Molecular Evolution on Divergence Estimates. PLoS ONE 8(12): e85240.
  • Leavitt SD, Divakar PK, Crespo A, Lumbsch HT (2016) A matter of time – understanding the limits of the power of molecular data for delimiting species boundaries. Herzogia 29: 479–492.
  • Leavitt SD, Kirika PM, Amo de Paz G, Huang JP, Hur JS, Elix JA, Grewe F, Divakar PK, Lumbsch HT (2018) Assessing phylogeny and historical biogeography of the largest genus in lichen-forming fungi, Xanthoparmelia (Parmeliaceae, Ascomycota). Lichenologist 50: 299–312.
  • Lücking R (2012) Predicting species richness in tropical lichenized fungi with ‘modular’ combinations of character states. Biodiversity and Conservation 21: 2341–2360.
  • Lücking R, Hodkinson BP, Leavitt SD (2016) The 2016 classification of lichenized fungi in the Ascomycota and Basidiomycota – Approaching one thousand genera. Bryologist 119: 361–416.
  • Lumbsch HT (2002) Analysis of phenolic products in lichens for identication and taxonomy. In: Kranner I, Beckett R, Varma A (Eds) Protocols in Lichenology Culturing, biochemistry, ecophysiology and use in biomonitoring. Springer, Berlin, 281–295.
  • Lumbsch HT, Huhndorf SM (2010) Myconet Volume 14. Part one. Outline of Ascomycota – 2009. Fieldiana Life and Earth Sciences 1: 1–42.
  • Mangold A, Martín MP, Lücking R, Lumbsch HT (2008) Molecular phylogeny suggests synonymy of Thelotremataceae within Graphidaceae (Ascomycota: Ostropales). Taxon 57: 476–486.
  • Nash III TH (1974) Two New Species of Xanthoparmelia with Diffractaic Acid. Bryologist 72: 234–235.
  • Nash III TH, Elix JA (2004) Xanthoparmelia. In: Nash III TH, Ryan BD, Diederich P, Gries C, Bungartz F (Eds) Lichen Flora of the Greater Sonoran Desert Region. Vol. II. Lichens Unlimited, Arizona State University. Tempe, Arizona, 566–605.
  • Nash III TH, Herrera-Campos MA, Elix JA (2016) Xanthoparmelia in Mexico. Bibliotheca Lichenologica 110: 621–641.
  • Orange A, James PW, White FJ (2010) Microchemical methods for the identification of lichens, second edition with additions and corrections. British Lichen Society, London, 1–101.
  • Schmitt I, Crespo A, Divakar PK, Fankhauser JD, Herman-Sackett E, Kalb K, Nelsen MP, Nelson NA, Rivas-Plata E, Shimp AD, Widhelm T, Lumbsch HT (2009) New primers for promising single-copy genes in fungal phylogenetics and systematics. Persoonia 23: 35–40.
  • Thell A, Crespo A, Divakar PK, Kärnefelt I, Leavitt SD, Lumbsch HT, Seaward MRD (2012) A review of the lichen family Parmeliaceae – history, phylogeny and current taxonomy. Nordic Journal of Botany 30: 641–664.
  • Troia MJ, McManamay RA (2016) Filling in the GAPS: evaluating completeness and coverage of open-access biodiversity databases in the United States. Ecology and Evolution 6: 4654–4669.
  • Vilgalys R, Hester M (1990) Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. Journal of Bacteriology 172: 4238–4246.
  • White TJ, Bruns TD, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (Eds) PCR Protocols. Academic Press, San Diego, 315–322.
  • Zoller S, Scheidegger C, Sperisen C (1999) PCR primers for the amplification of mitochondrial small subunit ribosomal DNA of lichen-forming ascomycetes. Lichenologist 31: 511–516