ARTICLE
167
© 2018 In e na ional Mycological Associa ion
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VOLUME 9 · NO. 1
Conside a ions and consequences o allowing DNA sequence da a as ypes
o ungal axa
Juan Ca los Zamo a1, Måns S ensson1, Roland Ki schne 2, Ibai Ola iaga3, S engunna Ryman1, Luis Albe o Pa a4, Józse
Geml5, Anna Rosling6 , Sla omí Adamčík*, Teu o Ah i, M. Ca he ine Aime, A. Ma yn Ainswo h, László Albe , Edga do Albe ó,
Albe o Al és Ga cía, Dmi y Agee , Reinha d Age e , Begoña Agui e-Hudson, Joe Ammi a i, Ha y Ande sson, Claudio Angelini,
Vladimí An onín, Takayuki Aoki, And é Ap oo , Didie A gaud, Blanca Imelda A guello Sosa, A ne A onsen, Ul A up, Bi a Asga i,
Bo is Assyo , Viole a A ienza, Di e Bandini, João Luís Bap is a-Fe ei a, Hans-O o Ba al, Tim Ba oni, Robe Weinga Ba e o,
Hen y Beke , Ann Bell, Jean-Michel Bellange , F ancesco Bellù, Ma in Bemmann, Mika Bendiksby, Egil Bendiksen, Ka iina
Bendiksen, Lajos Benedek, Anna Bé ešo á-Gu o á, F anz Be ge , Reinha d Be nd , Anna osa Be nicchia, Alona Yu. Bike o a,
En ico Bizio, Cu is Bjo k, Teun Boekhou , Da id Boe mann, Tanja Böhning, Flo en Boi in, Ca los G. Boluda, Menno W.
Boomslui e , Jan Bo o ička, To E ik B and ud, Uwe B aun, I win B odo, Ta iana Bulyonko a, Ha old H. Bu dsall J ., Ba Buyck,
Ana Rosa Bu gaz, Vicen Cala ayud, Philippe Callac, Emanuele Campo, Massimo Candusso, B igi e Capoen, Joaquim Ca bó,
Ma eo Ca bone, Ra ael F. Cas añeda-Ruiz, Michael A. Cas ellano, Jie Chen, Philippe Cle c, Gio anni Consiglio, Gilles Co iol,
Régis Cou ecuisse, Ana C espo, Ca hy C ipps, Ped o W. C ous, Glads one Al es da Sil a, Mei iele da Sil a, Ma jo Dam, Nico
Dam, F ank Dämm ich, Kanad Das, Linda Da ies, Eske De C op, And e De Kesel, Ruben De Lange, Bá ba a De Mad ignac
Bonzi, Thomas Edison E. dela C uz, Lynn Delga , Vincen Demoulin, Dennis E. Desja din, Paul Diede ich, Bálin Dima, Ma ia
Ma ha Dios, P adeep Kuma Di aka , Clo is Douanla-Meli, B ian Douglas, Elisand o Rica do D echsle -San os, Paul S. Dye ,
U sula Ebe ha d , Damien E z, Fe nando Es e e-Ra en ós, Ja ie Angel E ayo Salaza , Ve a E enson, Guillaume Eyssa ie ,
Edi Fa kas, Alain Fa e, Anna G. Fedoso a, Ma io Filippa, Pé e Finy, Adam Flakus, Simón Fos, Jacques Fou nie , And é
F ai u e, Paolo F anchi, Ana Espe anza F anco Molano, Ge no F iebes, And eas F isch, Alan F yday, Giuliana Fu ci, Rica do
Galán Má quez, Ma eo Ga belo o, Joaquina Ma ía Ga cía-Ma ín, Mónica A. Ga cía O álo a, Dania Ga cía Sánchez, Alain
Ga dienne , Sigis edo Ga nica, Isaac Ga ido Bena en , Gene ie e Ga es, Alice da C uz Lima Ge lach, Masoomeh Ghobad-
Nejhad, Ta iana B. Gibe oni, Tine G ebenc, I mga d G eilhube , Bella G ishkan, Johannes Z. G oenewald, Ma in G ube, Gé ald
G uhn, Cécile Gueidan, G o Gulden, Luis FP Gusmão, Jose Ha ellne , Michel Hai aud, Ma ek Halama, Nils Hallenbe g, Roy E.
Halling, Ka en Hansen, Ch is o e Bugge Ha de , Jacob Heilmann-Clausen, S ip Helleman, Alain Hen io , Ma ga i a He nandez-
Res epo, Raphaël He e, Ca oline Hoba , Mascha Ho meis e , Klaus Høiland, Jan Holec, Håkon Holien, Ka en Hughes, Vi
Hubka, Seppo Huh inen, Bo is I anče ić, Ma ian Jage s, Wal e Jakli sch, AnnaElise Jansen, Ru ishika S. Jayawa dena, Thomas
S je negaa d Jeppesen, Mikael Jeppson, Pe e Johns on, Pe Magnus Jø gensen, Ing a Kä ne el , Liudmila B. Kalinina, Gin a as
Kan ilas, Mi ko Ka adele , Taiga Kasuya, I ona Kau mano á, Richa d W. Ke igan, Ma in Ki chmai , Anna Kiyashko, Dániel G.
Knapp, Henning Knudsen, Ke y Knudsen, Tommy Knu sson, Mi osla Kolařík, U mas Kõljalg, Alica Košu ho á, A ila Koszka,
Heikki Ko i an a, Ve a Ko ko a, Ondřej Koukol, Jiří Kou , Gábo M. Ko ács, Ma in Kříž, Åsa K uys, Vik o Kuče a, Linas Kudzma,
F ancisco Kuha , Ma in Kukwa, T. K. A un Kuma , Vladimí Kunca, I ana Kušan, Thomas W. Kuype , Ca los Lado, Thomas
Læssøe, Pa ice Lainé, Ewald Lange , Ellen La sson, Ka l-Hen ik La sson, Ga y Lau sen, Ch is ian Lecha , Se ena Lee, James
C. Lendeme , Lau a Le in, Uwe Lindemann, Håkan Linds öm, Xingzhong Liu, Regulo Ca los Lla ena He nandez, Es e e Llop,
Csaba Locsmándi, Debo ah Jean Lodge, Michael Loizides, László Lőkös, Jenni e Luangsa-a d, Ma hias Lüde i z, Tho s en
Lumbsch, Ma hias Lu z, Dan Mahoney, Eka e ina Malyshe a, Ve a Malyshe a, Pa inja e ee il Manimohan, Yasmina Ma in-Felix,
Guilhe mina Ma ques, Rubén Ma ínez-Gil, Guy Ma son, Ge a do Ma a, P. B andon Ma heny, Gei Ha ald Ma hiassen, Ne en
Ma očec, Helmu May ho e , Mehdi Meh abi, I eneia Melo, A min Mešić, And ew S. Me h en, O o Mie inen, Ana M. Millanes
Rome o, And ew N. Mille , James K. Mi chell, Roland Mobe g, Pie e-A hu Mo eau, Gab iel Mo eno, Olga Mo ozo a, Asunción
Mo e, Lucia Muggia, Guille mo Muñoz González, Leena Myllys, Is án Nagy, László G. Nagy, Ma ia Alice Ne es, Tuomo Niemelä,
Pie Luigi Nimis, Nicolas Ni ei o, Machiel E. Noo deloos, Ande s No din, Sa a Raouia Noumeu , Yu i No ozhilo , Jo inde Nuy inck,
Es e i Ohenoja, Pa icia Oli ei a Fiuza, Alan O ange, Alexande O dyne s, Bea iz O iz-San ana, Le icia Pacheco, Fe enc Pál-
Fám, Melissa Palacio, Zdeněk Palice, Vik o Papp, Kad i Pä el, Julia Pawlowska, Au elia Paz, U sula Pein ne , Shaun Pennycook,
Olin o Lipa ini Pe ei a, Pablo Pé ez Daniëls, Miquel À. Pé ez-De-G ego io Capella, Ca los Manuel Pé ez del Amo, Se gio Pé ez
Go jón, Se gio Pé ez-O ega, Is ael Pé ez-Va gas, B ian A. Pe y, Jens H. Pe e sen, Ronald H. Pe e sen, Donald H. P is e ,
Chayana d Phukhamsakda, Ma cin Pią ek, Meike Piepenb ing, Raquel Pino-Bodas, Juan Pablo Pinzón Esqui el, Paul Pi o ,
Eugene S. Popo , O lando Popo , Ma ía P ie o Ál a o, Ch is ian P in zen, Nadezhda Psu se a, Wi oon Pu ahong, Luis Quijada,
Ge ha d Rambold, Na alia A. Ramí ez, Huze a Raja, Oli ie Raspé, Tania Raymundo, Ma ina Réblo á, Yu y A. Reb ie , Juan
de Dios Reyes Ga cía, Miguel Ángel Ribes Ripoll, F anck Richa d, Mike J. Richa dson, Víc o J. Rico, Ge a do Lucio Robledo,
Fla ia Rod igues Ba bosa, C is ina Rod iguez-Caycedo, Pamela Rod iguez-Flakus, Anna Ronikie , Luis Rubio Casas, Ka e ina
Ruse ska, Gün e Saa , I ja Saa , Isabel Salcedo, Se gio M. Salcedo Ma ínez, Ca los A. Sal ado Mon oya, San iago Sánchez-
doi:10.5598/ima ungus.2018.09.01.10 IMA FUNGUS · 9(1): 167–175 (2018)
Zamo a e al.
ARTICLE
168 IMA FUNGUS
Ramí ez, J. Vladimi Sando al-Sie a, Se gi San ama ia, Josiane San ana Mon ei o, Hans Jose Sch oe s, Ba ba a Schulz, Gee
Schmid -S ohn, T ond Schumache , Bea ice Senn-I le , Hana Še číko á, Oleg Shchepin, Takashi Shi ouzu, An on Shi yae ,
Klaus Siepe, Es eban B. Si , Mohammad Soh abi, Ka l Soop, Viachesla Spi in, Toby Sp ibille, Ma c S adle , Joos S alpe s,
Soili S en oos, A e Suija, S ellan Sunhede, S en S an esson, Sig a d S ensson, Ta yana Yu. S e ashe a, K zysz o Świe kosz,
Heidi Tamm, Ha i a Taskin, Ad ien Taudiè e, Jan-Olo Tedeb and, Raúl Tena Lahoz, Ma ina Temina, A ne Thell, Ma co Thines,
Gö an Tho , Holge Thüs, Lei Tibell, Sanja Tibell, Eina Timdal, Zdenko Tkalčec, To Tønsbe g, Gé a d T ichies, Dagma T iebel,
And ei Tsu ykau, Rodham E. Tulloss, Vee a Tuo inen, Miguel Ulloa Sosa, Ca los U celay, F ançois Valade, Rica do Valenzuela
Ga za, Pie e an den Boom, Nicolas Van Voo en, Aida M. Vasco-Palacios, Jukka Vau as, Juan Manuel Velasco San os, Else
Vellinga, Annemieke Ve beken, Pe Ve lesen, Al edo Vizzini, He mann Voglmay , Se gey Volobue , Wol gang on B ackel, Elena
Vo onina, G i Wal he , Roy Wa ling, E i Webe , Ma s Wedin, Øy ind Wehol , Ma in Wes be g, Eugene Yu chenko, Pe Zehnálek,
Huang Zhang, Mikhail P. Zhu benko, and S e an Ekman1
1Museum o E olu ion, Uppsala Uni e si y, No by ägen 16, 75236 Uppsala, Sweden; co esponding au ho e-mail: [email p o ec ed]
2Na ional Cen al Uni e si y, Taoyuan Ci y, Taiwan
3Uni e sidad Rey Juan Ca los, 28933 Mós oles, Mad id, Spain
4A enida Pad e Cla e 7, 5º G, 09400 A anda de Due o, Bu gos, Spain
5Na u alis Biodi e si y Cen e , Vondellaan 55, 2332AA Leiden, The Ne he lands
6E olu iona y Biology Cen e, Uppsala Uni e si y, No by ägen 18D, 75236 Uppsala, Sweden
*A i s e sion o his ex was p epa ed by he i s eigh au ho s and he las one. The o he lis ed co-au ho s suppo he con en , and hei
ac ual con ibu ions a ied om only suppo o addi ions ha subs an ially imp o ed he con en . The ull de ails o all co-au ho s, wi h hei
a ilia ions, a e included in Supplemen a y Table 1 o easons o cla i y and space.
Abs ac : Nomencla u al ype de ini ions a e one o he mos impo an concep s in biological nomencla u e.
Being physical objec s ha can be e-s udied by o he esea che s, ypes pe manen ly link axonomy (an a i icial
ag eemen o classi y biological di e si y) wi h nomencla u e (an a i icial ag eemen o name biological di e si y).
Two p oposals o amend he In e na ional Code o Nomencla u e o algae, ungi, and plan s (ICN), allowing DNA
sequences alone (o any egion and ex en ) o se e as ypes o axon names o ouche less ungi (mainly pu a i e
axa om en i onmen al DNA sequences), ha e been submi ed o be o ed on a he 11 h In e na ional Mycological
Cong ess (Pue o Rico, July 2018). We conside a ious gene ic p ocesses a ec ing he dis ibu ion o alleles among
axa and ind ha alleles may no consis en ly and uniquely ep esen he species wi hin which hey a e con ained.
Should he p oposals be accep ed, he meaning o nomencla u al ypes would change in a undamen al way om
physical objec s as sou ces o da a o he da a hemsel es. Such changes a e conduci e o i ep oducible science,
he po en ial ypi ica ion on a e ac ual da a, and massi e c ea ion o names wi h low in o ma ion con en , ul ima ely
causing nomencla u al ins abili y and unnecessa y wo k o u u e esea che s ha would s all u u e explo a ions
o ungal di e si y. We conclude ha he accep ance o DNA sequences alone as ypes o names o axa, unde he
e ms used in he cu en p oposals, is unnecessa y and would no sol e he p oblem o naming pu a i e axa known
only om DNA sequences in a scien i ically de ensible way. As an al e na i e, we highligh he use o o mulas o
naming pu a i e axa (candida e axa) ha do no equi e any modi ica ion o he ICN.
A icle in o: Submi ed: 14 May 2018; Accep ed: 21 May 2018; Published: 24 May 2018.
INTRODUCTION
Hawkswo h e al. (2016) ecen ly submi ed a se o p oposals
o modi y he In e na ional Code o Nomencla u e o algae,
ungi, and plan s (ICN), aimed a allowing DNA sequences
wi hou ouche ed specimens o se e as ypes o ungal
axon names. These p oposals we e i s ejec ed by he
Nomencla u e Commi ee o Fungi (see Tu land & Wie sema
2017) and subsequen ly by he XIX In e na ional Bo anical
Cong ess (IBC) in Shenzhen, China, in 2017. A he same
ime, a Special-pu pose Commi ee on DNA sequences as
ypes was p oposed o explo e and ca e ully discuss his
issue, pa ing he way o u he deba e du ing he nex IBC
in Rio de Janei o in 2023 (Tu land e al. 2017).
Howe e , appa en ly because o a pe cei ed u gency in
he es ablishmen o a sys em o naming pu a i e new axa
known only om DNA sequences, he same p oposals we e
ecen ly e-published (Hawkswo h e al. 2018) wi h he in en
ha hey be discussed and o ed on a he o hcoming 11 h
In e na ional Mycological Cong ess (IMC11) in Pue o Rico in
July 2018. The p oposals aim a allowing he o mal naming
o ungal axa only known by DNA sequences ( he “da k
ma e ungi” o G ossa e al. 2016), by au ho izing he DNA
sequence i sel o be he ype o a axon name in he absence
o a specimen.
The ICN a emp s o c ea e “ he p o ision o a s able
me hod o naming axonomic g oups, a oiding and ejec ing
he use o names ha may cause e o and ambigui y o
h ow science in o con usion” (P eamble 1). This p o ision
elies on he use o he nomencla u al ype, “ he ace — he
desicca ed, la ened ace o be su e, bu s ill he ace — ha
is a ached o he name o a species” (Das on 2004).
In ou opinion, he ungal-speci ic amendmen s p oposed
o he ICN by Hawkswo h e al. (2018) should be ejec ed on
Key wo ds:
IMC11
nomencla u e
specia ion
axonomy
ypi ica ion
ouche less ungi
Consequences o allowing sequence da a as ypes
ARTICLE
169
VOLUME 9 · NO. 1
he g ounds ha hey would ha e majo nega i e implica ions
o ungal nomencla u e and sys ema ics, o mo e speci ically,
iola e P eamble 1, p omo e i ep oducible science, and
undamen ally change he meaning o he ype concep
compa ed o how i has been applied du ing he las cen u y.
An in o med deba e is needed o a oid any unwan ed e ec s
o a ushed decision.
THE PROPOSALS
The p oposals o Hawkswo h e al. (2018) in end o inse a
single a icle, A . F.4.2, h ough p oposal (F-005), ollowed
by h ee ecommenda ions, Rec. F.4A.1-3, h ough p oposal
(F-006). As only A . F.4.2 would be manda o y, i is c ucial o
e alua e p oposal (F-005) in pa icula de ail: “(F-005) Inse
a new pa ag aph a e A . F.4.1 as ollows: F.4.2. In ungi,
when DNA sequence da a co esponding o a new axon
ha e been de ec ed, bu no physical specimen has been
ound o se e as he ype o he name o he new axon (A .
8.1–8.4), he ype may be composed o DNA sequence da a
deposi ed in a public eposi o y.”
The ecommenda ions ha ollow sugges , in summa y,
ha “ he new axon should be desc ibed wi h e e ence o
a published phylogene ic analysis” (Rec. F.4A.1), ha he
new axon “should be ep esen ed by mul iple sequences
ob ained in independen s udies” (Rec. F.4A.2), and ha he
sequence should de i e om “ he molecula egions ha a e
app op ia e o delimi ing species” (Rec. F.4A.3). These a e
me ely ecommenda ions, howe e , and need no be ollowed
(as emphasized by Tu land & Wie sema 2017).
SPECIES VERSUS DNA SEQUENCES
I has been a gued ha “ he Code se es only o egula e
he alid publica ion o names, no o pass judgmen on he
scien i ic hypo heses embodied in names” (He e al. 2015).
Al hough nomencla u e can be seen as a “ ema kable ac o
applied me aphysics” (Das on 2004), he ci cumsc ip ion o
he axa being named is a undamen ally scien i ic p ocess.
The p oposal ecommends ha a new axon “be desc ibed
wi h e e ence o a published phylogene ic analysis” (Rec.
F.4A.1 o p oposal F-006). This wo ding implies ha i is
possible o i s ci cumsc ibe a new axon by phylogene ic
analysis, hen name he new axon using a DNA sequence
ype ha can be unequi ocally associa ed wi h he new
axon. Fo he easons ou lined below, his may no eadily
be he case a he le el o species in ecombining o ganisms,
which we suspec is whe e A . F.4.2 is mos equen ly going
o be applied.
Assuming ha species a e unde s ood as somehow
sepa a ely e ol ing uni s (e.g. de Quei oz 1998, 2005,
2007, Hey 2006), hey can, soone o la e a e o ma ion,
be de ec ed using a a ie y o me hods (o en misleadingly
e med ‘species concep s’; Hey 2006), e.g. ep oduc i e
isola ion ( he ‘biological species concep ’), mo phology, o
genealogical monophyly wi h o wi hou auxilia y c i e ia like
conco dance among genes (co esponding o he gene ic
e sions o ‘phylogene ic species concep ’). Du ing a simple
di e gence o one ances al species in o wo daugh e
species, (nea ly) neu al loci will inhe i andom samples
o alleles om he ances al species, some o which a e
likely o be sha ed ac oss he daugh e species (ances al
polymo phisms). Gi en ime, ances al alleles will go ex inc
andomly and new alleles will a ise, in he mos likely case
causing species o appea non-monophyle ic on he gene
ees. Finally, species will achie e ecip ocal monophyly on
he gene ees. This p ocess has been known and desc ibed
in he li e a u e o decades (e.g. Tajima 1983, Takaha a &
Nei 1985, Neigel & A ise 1986, Nei 1987, Pamilo & Nei
1988, Takaha a 1989, A ise & Ball 1990, Hudson e al.
1992, Hey 1994, Ha ison 1998, A ise 2000, Hudson &
Coyne 2002, Rosenbe g 2003, Coyne & O 2004, Naci i
& Linde 2015) and has been elegan ly explained and
illus a ed by, o example, Leliae e al. (2014). The lag
ime om lineage di e gence un il ecip ocal monophyly
in neu al loci will depend on he e ec i e popula ion size,
gene a ion ime, and popula ion s uc u e (Hudson 1990,
Wakeley 2000) and i s du a ion will a y s ochas ically
be ween nuclea loci in ecombining o ganisms (Hudson &
Tu elli 2003). Ob iously, any species ecogni ion p o ocol
equi ing ecip ocal monophyly will only be able o de ec
he species long a e hey di e ged (Hudson & Coyne
2002). Posi i e selec ion can subs an ially sho en he ime
i akes o emo e ances al polymo phisms and inally
each ecip ocal monophyly. The p opo ion o he genome
unde going posi i e selec ion du ing and a e specia ion
appea s o be small, howe e , p obably eaching a mos
a ew pe cen (e.g., 1.1 and 1.7 % o he genes in humans
and chimpanzee, espec i ely; Bakewell e al. 2007). As an
aside, he s ochas ic p ocess inally leading o ecip ocal
monophyly in he indi idual genes also means ha he e
canno exis a uni e sal di e gence h eshold o delimi ing
ungal (o o he ) species using DNA sequences, no o he
e y widely used in e nal ansc ibed space (ITS) egion in
ungi (e.g. Nilsson e al. 2008, Bado i e al. 2017), no any
o he DNA egion in any o ganism g oup (e.g. Meie e al.
2006 conce ning me azoans).
Gene his o ies, a s anda d p oduc in applied phylo-
gene ics, canno au oma ically be equa ed wi h he species
his o y (e.g. Tajima 1983, Pamilo & Nei 1988, Maddison
1997, Knowles & Ca s ens 2007). The e is no eason o
hink ha any DNA egion o any o ganism g oup is ee o
mechanisms ha c ea e a disco dance be ween he gene
and species his o ies. Such mechanisms ha e been ound
o be widesp ead ac oss he ee o li e (e.g. So a & Vogle
2001, Rau enbe g e al. 2008, Blanco-Pas o e al. 2012,
Ku sche a e al. 2014, Lamichhaney e al. 2015, Ga ido e
al. 2017, Kud ya se a & Gladkikh 2017, Meye e al. 2017,
Pa ks e al. 2017, Pey égne e al. 2017, Vd’ačný 2017).
Incong uence be ween gene his o ies, demons a ing ha
a leas some o hem mus be di e en om he his o y o
he species, has indeed also been demons a ed o occu in
he ungi (e.g. O’Donnell & Cigelnik 1997, Sung e al. 2007,
Ha de e al. 2013, Al e mann e al. 2014, Saag e al. 2014,
S ewa e al. 2014). A con lic be ween he gene his o ies
and species his o y is no only caused by he andomness
o gene ic d i desc ibed abo e. O he mechanisms, all
obse ed also in ungi, obscu e ela ionships among axa
Zamo a e al.
ARTICLE
170 IMA FUNGUS
and some ( he i s h ee) ha e he po en ial o cause non-
iden i iabili y o a single DNA sequence: he exchange
o en i e nuclei be ween he e ospeci ic ungal syncy ia,
ho izon al gene ans e , hyb idiza ion (some imes ollowed
by in og ession o allopolyploidy), gene duplica ion
(including also pseudogene and num o ma ion), and
in a-indi idual a iabili y in he ibosomal DNA epea
caused by limi s o conce ed e olu ion (Dean e al. 2005,
Ru hs & Nakhleh 2005, Je oy e al. 2006, Nea sey e al.
2010, Ellison e al. 2011, Lindne & Banik 2011, Rope e
al. 2011, Hughes e al. 2013, Li e al. 2013, Lindne e al.
2013, Gladieux e al. 2014, Som 2014, Naci i & Linde 2015,
Shapi o e al. 2016, Thié y e al. 2016, Fou ie e al. 2017,
Li e al. 2017, Hughes e al. 2018, S eenkamp e al. 2018).
Ob iously, species delinea ions gene a ed om a single
ma ke canno be e alua ed using da a om he same
ma ke , because ha would make he a gumen ci cula .
We conclude ha a DNA sequence o an allele canno
be seen as “co esponding o” any axon ( he wo ding o he
p oposal), bu ep esen s he di e si y o alleles o he gene
om which i was de i ed. An allele canno be expec ed o
be unique o he species om which i was de i ed and we
canno know whe he o no alleles a e unique o a species
when sequence da a a e only a ailable om a single o a
limi ed numbe o ma ke s and indi iduals (e.g. he popula
ITS ba code in ungi; Schoch e al. 2012, Bado i e al.
2017). “I species membe ship is con ingen o o ganisms
in gene al, i ough o be con ingen o hose chosen as he
ype specimens o hei species” (Le ine 2001). Ha ing said
ha , some o hese pi alls a e mo e easily de ec ed and
emedied when he numbe o ma ke s is high and me hods
designed o handle hem (including bu no limi ed o e sions
o he ‘phylogene ic analysis’ p esc ibed by Rec. F.4A.1) a e
applied (Dupuis e al. 2012, Fuji a e al. 2012).
IMPACT ON NOMENCLATURAL TYPES
(SPECIMENS VERSUS DNA SEQUENCES)
An accep ance o he p oposal would undamen ally al e he
meaning o nomencla u al ypes. This is because ins ead o
using a physical objec as he ype o a name, we would jus
use in o ma ion om a cha ac e o he o ganism as he ype.
Indeed, he pa allel o he designa ion o a DNA sequence as
a ype would be he designa ion o in o ma ion ex ac ed om
o ganisms (specimens) as ypes, no wi h he designa ion o
specimens as ypes. In o he wo ds, his would be akin o
designa ing a sample o spo e measu emen s as he ype o
an o ganism. I should be no ed ha he possibili y o selec
a desc ip ion as a ype exis ed be o e he publica ion o he
Be lin Code in 1988. Howe e , his op ion was e en ually
ejec ed by he scien i ic communi y, and emo ed om he
Be lin Code wi h his no e in he P e ace: ”The p o ision
ha exis ed o a ype o be a desc ip ion unde ce ain
ci cums ances — some hing ha many el amoun ed o a
epudia ion o he ype me hod — has been dele ed om he
Code” (G eu e e al. 1988: iii).
Names o axa a e applied o o ganisms, no o cha ac e s
o hose o ganisms. The e o e, a physical objec should
p e e ably se e as he ype o a name, a he han he
cha ac e is ics o ha objec . By allowing al eady ex ac ed
da a, such as a DNA sequence, o se e as ype ins ead o
he sou ce o he da a, new in o ma ion canno be ob ained
when his is equi ed (see below). In addi ion, we suspec ha
bypassing he cu en concep o a ype is o en unnecessa y,
because echniques exis o isualize ungal DNA wi h high
speci ici y (Baschien e al. 2001, Beh ens e al. 2003, Inácio
e al. 2003, Baschien e al. 2008, Vági e al. 2014, Sp ibille e
al. 2016). Al hough no ye s anda d pa s o he mycological
oolbox, such echniques can wi h ela i e ease be applied o
loca e physical specimens e en o axa ha canno cu en ly
be cul i a ed.
Acco ding o he ICN, a nomencla u al ype is “ ha
elemen o which he name o a axon is pe manen ly
a ached, whe he as he co ec name o as a synonym”
(A . 7.2). Fo species-le el axa and in aspeci ic axa,
which a e he basic uni s in axonomy, a ype is “ei he a
single specimen conse ed in one he ba ium o o he
collec ion o ins i u ion, o an illus a ion” (A . 8.1). Why
ha e esea che s ag eed o keep hese de ini ions o such
a long ime? The answe is s aigh o wa d: because ypes
a e an almos ne e -ending sou ce o in o ma ion, as hey
can be analyzed by di e en people using di e en me hods
and hus p o ide new answe s. E e y ime a ype specimen
is e-examined, he e is an oppo uni y o ex ac new
in o ma ion, which may be use ul o sol ing p oblems ha
a e cons an ly a ising as ou knowledge inc eases. Mos
ypes a e specimens (especially nowadays) because a
specimen o any li ing o ganism is such a complex en i y ha
i is ha d o imagine us being able o ex ac all he possible
in o ma ion con ained in i . These p ope ies ha e al eady
been conside ed in an edi o ial o IMA Fungus w i en by
he P esiden o he In e na ional Mycological Associa ion
(Sei e 2017). The e o e, e en hough he p oblem o non-
unique cha ac e s used o diagnosis is no es ic ed o
sequence da a, he c ucial dis inc ion om mo phological
desc ip ions o biological ype specimens is ha ha ing a
DNA sequence as ype i ually p ecludes he ob aining o
any new in o ma ion o esol e any axonomic p oblems.
In con as , e en illus a ions, which a e now accep ed as
ypes only in e y speci ic si ua ions (see A . 40.5 o he
cu en use o hese) and inc easingly alling in o disuse,
may be a sou ce o o e looked in o ma ion.
Epi ype selec ion may be seen as a possible solu ion
in he expec ed cases when he DNA sequence alone is
insu icien o he p ecise applica ion o he name o a axon
(Rybe g & Nilsson 2018). Epi ypi ica ion was concei ed as
a p ac ical solu ion in cases when he ype o a name u ns
ou o be ambiguous (ICN, A . 9.8). Epi ypes a e equen ly
designa ed o old names, and hey a e no ee o undesi ed
p oblems a ec ing nomencla u al s abili y (Rindi e al. 2017).
Epi ypi ica ions ha e o be based on an exis ing ype, and
a e o en being made because ou knowledge o he p esen
echnology a e he limi s o ex ac ing he needed in o ma ion
om he ype ha al eady exis s. Those limi a ions may be
o e come by o he esea che s o by new echnologies in he
u u e. Fo DNA sequence da a, he ype i sel would always
be he limi ing bo leneck, ega dless o he esea che ’s
skills o he p og ess o science.
Consequences o allowing sequence da a as ypes
ARTICLE
171
VOLUME 9 · NO. 1
IMPACT ON NAMES OF TAXA AND FUTURE
TAXONOMIC STUDIES
The main a gumen used by Hawkswo h e al. (2016), o
jus i y he u gency o allowing DNA sequences as ypes, is
ha axa only known om DNA sequences “ equi e scien i ic
names in o de o acili a e communica ion abou hem”. While
esea che s indeed need names o axa o communica e
among colleagues and wi h he gene al public, hose names
a e linked o in o ma ion ha makes hem use ul, like biology,
dis ibu ion, ecology, mo phology, physiology, pa hology, e c.
(C ous e al. 2015). In o he wo ds, we a e using scien i ic
names because hey a e meaning ul o a wide ange o
people.
In addi ion, axonomis s a e awa e ha an inc eased
numbe o alidly published names will no necessa ily
acili a e communica ion. On he con a y, in he no uncommon
si ua ion in which he same axon has been named on se e al
occasions, much con usion may a ise un il he iden i y o
hose names is inally se led. Indeed, axa based solely on
DNA sequences no p ecisely ma ching any o hose p esen
in public eposi o ies ha e al eady been desc ibed and
allen in o mo e o less immedia e synonymy, because he
necessa y compa isons wi h p e iously desc ibed axa we e
no unde aken (Gams 2016). The p oposals would p omo e
such bad p ac ice.
An undesi ed side-e ec ha should also be conside ed
is ha , in p ac ice, ew esea che s will be de o ed o e-
desc ibing (o ac ually desc ibing) species ha ha e been
p e iously named based on jus a DNA sequence. This
has se e al causes, bu among hem, he e is an impo an
bias in esea ch jou nals dis a o ing he publica ion o e-
desc ip ions o al eady known axa, e sus he desc ip ion o
new axa. Ano he eason is ime cons ain s, since i is no
uncommon ha specialis s do no ha e he ime o p ope ly
desc ibe all o he nume ous undesc ibed species hey a e
awa e o . This makes hem ocus on hose ha a e mo e
likely o be published as new species and no on hose ha
ha e been al eady desc ibed, e en i p e ious desc ip ions
a e aul y o de ec i e. Anyhow, ha ing nume ous names
only based on DNA sequences and ew desc ip ions o he
ac ual o ganisms would c ea e an eno mous numbe o
alidly published names applied o axa o which i ually no
in o ma ion exis s.
RELIABILITY AND EXTENT OF DATA
The p oposed A . F.4.2. e ec i ely means ha any DNA
sequence o any egion and ex en , gene a ed by any
p ocedu e o aken om a public eposi o y, could se e as
he ype o a name o a axon somehow indica ed o be new.
In p ac ice, he sequence selec ed as he ype could ange
om an oligonucleo ide o he en i e genome. The p oposal
p o ides e y li le guidance, excep o he ecommenda ions
ha he ype sequence should be ep esen ed by “mul iple
sequences” and ha he selec ed ma ke should be
“app op ia e o delimi ing species” (p oposed Rec. F.4A.2,
F.4A.3). I is no clea wha ‘mul iple’ means o how a
ma ke is es ablished as uni e sally ‘app op ia e’. One can
in e , howe e , ha he ‘app op ia e’ ma ke will, in mos
applica ions, be he ITS egion, which has been dubbed as
he p ima y ba code ma ke in ungi (Schoch e al. 2012).
A majo conce n is he eliabili y o he DNA sequence
da a (B idge e al. 2003, Nilsson e al. 2006). PCR o
cloning e o s (including he in oduc ion o chime as), DNA
deg ada ion, and pos -p ocessing o ch oma og ams, ha e
been shown o be a sou ce o sequence a ia ion in a leas
some g oups (Haas e al. 2011, Sando al-Sie a e al. 2014,
Hughes e al. 2015, S id e al. 2015, Aas e al. 2017, Nilsson
e al. 2017, Thielecke e al. 2017, Bieke & Ma in 2018).
Such DNA sequences a e no eal and canno be checked
o co ec ed wi hou access o a physical specimen o , as
a minimum, access o he aw sequence eads (T ipp &
Lendeme 2014). I accep ed as ypes, his means mycology
would emb ace i ep oducible science.
The conce ns ou lined he e, in combina ion wi h he isk
o compa ing non-o hologous sequences o incomple ely
conce ed copies o he ibosomal DNA, a e eally abou
scien i ic quali y and no nomencla u e pe se. Howe e ,
nomencla u e assumes ha axa a e i s delinea ed, hen
named. The p oposal, i implemen ed, would isk opening he
loodga es o poo da a and ques ionable scien i ic p ac ice
being ansla ed in o o mally named axa ha will h ow
ungal axonomy in o pa alysis and dis epu e.
CANDIDATE NAMES
I we eally wan o s i e o a comp ehensi e code o
nomencla u e able o co e all li ing o ganisms, i is
necessa y o conside he ules o he o he exis ing codes
o nomencla u e. Fo ou pu poses, hese a e mainly he
In e na ional Code o Zoological Nomencla u e (ICZN; Ride
e al. 1999) and he In e na ional Code o Nomencla u e o
P oka yo es (ICNP; Pa ke e al. 2015). Also, i is impo an
o conside he use o nomencla u e by specialis s in di e en
axonomic g oups. In gene al, we hink i is be e o s i e o
s anda diza ion o ules ins ead o sha pening he di e ences
be ween Codes. The goal should be o c ea e a solid code
o nomencla u e ha , some day, may pe haps co e all
li ing o ganisms wi h all hei peculia i ies (e.g. he BioCode
ini ia i e; G eu e e al. 2011, h p://www.bionomencla u e.
ne /biocode2011.h ml).
An in e es ing o mula conce ning axa ha canno be
p ope ly desc ibed unde he ules o a code o nomencla u e is
he use o he e m “Candida us”. O iginally, his wo king e m
was p oposed by Mu ay & Schlei e (1994), and soon a e
imp o ed by Mu ay & S ackeb and (1995) o “desc ibing
p oka yo ic en i ies o which mo e han a me e sequence is
a ailable bu o which cha ac e is ics equi ed o desc ip ion
acco ding o he Code a e lacking”. I was p oposed because,
unde he ules o he ICNP, a p oka yo ic o ganism can only
be alidly desc ibed i he ype, which in his case is a li ing
s ain, can be conse ed as an axenic cul u e. The e a e o
cou se housands o p oka yo ic axa ha a e no cul i able
in such a way. Many o hem can, howe e , be s udied wi h
ega d o mo phology, ecology, me abolism, DNA da a, e c.
Fo ungi, ha ing such addi ional in o ma ion o a pa icula
clus e o DNA sequences (ne e a single one), o se e al
Zamo a e al.
ARTICLE
172 IMA FUNGUS
DNA egions om he same o ganism (ul ima ely and ideally,
a comple e genome), would be essen ial o ensu e ha a ue
axon is being p o isionally named, and o comply wi h basic
scien i ic s anda ds.
The Candida us wo king e m has p o ed o be a good
solu ion o mic obiologis s who wan o espec he ules o
he ICNP as well as o apply use ul names o ce ain axa.
Being awa e ha impo an in o ma ion (e.g. a p ope li ing
s ain as ype) is lacking o allow a o mal desc ip ion, such
axa can be alida ed when he equi emen s o he ICNP
a e ul illed. The bes example o how well his al e na i e
nomencla u e wo ks is he Candida e Phyla Radia ion, a
huge, well-known and well-communica ed g oup o Bac e ia
ha was p oposed based on he combined in o ma ion o
hund eds o genomes, ob ained om single cells as well as
me agenomics (Hug e al. 2016, Danczak e al. 2017).
The al e na i e o using p elimina y names o axa only
known om DNA da a has al eady been p oposed by Öpik
e al. (2009) as “ i ual axa”, by Taylo (2011) as “ENAS
ungi”, by Kõljalg e al. (2013) as “species hypo hesis”, and
indeed also by Hibbe e al. (2011) as “candida e species”.
We hink his is an in e es ing idea ha should be u he
explo ed and discussed in he u u e. Such candida e names
can be e-e alua ed and possibly o mally desc ibed in he
u u e when enough in o ma ion has become a ailable o
p o ide a good axon desc ip ion (see also Sei e 2017).
Finally, hey could be used wi h some eedom, since no
speci ic ules wi hin he codes o nomencla u e apply o
in alidly published names. I a majo conce n abou ungi
only known om DNA sequences is ha “ hey do no en e
names-based axonomic da abases” (see He e al. 2015),
a easonably easy solu ion would be o allow he egis a ion
o candida e o pu a i e names in hose da abases, in he
p ocess making i clea ha hose names ha e no ye been
alidly published because one o mo e o he equi emen s
o alid publica ion a e lacking (e.g. h p://www.bac e io.
ne /-candida us.h ml o candida e names o p oka yo ic
axa).
CONCLUSIONS
We conside he p oposals by Hawkswo h e al. (2018)
highly p oblema ic o he ollowing easons:
● DNA sequence ypes will ha e a e y low in o ma ion
con en ; subsequen ex ac ion o addi ional da a o
e i ica ion o he al eady ex ac ed da a will no be
possible.
● Two di e en axa may sha e iden ical DNA sequences a
a gi en locus, e en o al eady es ed ba coding ma ke s.
Con e sely, no all membe s o a species can be assumed
o sha e he same DNA sequence a a speci ic locus.
● In aspeci ic (o e en in aindi idual) di e ences in he
DNA sequence o a ma ke may be compa able o o
exceed in e speci ic di e ences.
● Some DNA sequences gene a ed h ough di e en
sequencing echniques may be a i ac s and consequen ly
no ep esen eali y. The p oposal does no say any hing
abou da a alida ion o he han a ecommenda ion ha
he DNA sequence should be ep esen ed by ‘mul iple
sequences’.
● The p oposal p omo es he mechanical p oduc ion o
axon names based on mino sequence di e gence,
wi hou aking any o he da a (such as gene ic a iabili y o
al eady desc ibed axa) in o accoun . Much downs eam
ime will ha e o be spen by u u e mycologis s ga he ing
addi ional in o ma ion.
● As axa wi h DNA sequence ypes accumula e, he
desc ip ion o a new species will be inc easingly di icul
wi hou DNA sequence da a. Desc ibing new species
based on he mo phology o unsequenced ma e ial will
in p ac ice no be easible i he possibili y exis s ha his
species has been desc ibed based on a DNA sequence.
● Since he p oposals allow any pa o he genome o be
used as a DNA ype, si ua ions in which di e en axa
may ha e been desc ibed using di e en pa s o he
genome will o ce esea che s o sequence a a ie y o
loci o es ablish whe he an ea lie name al eady exis s.
Likewise, a single axon may be desc ibed as no el
se e al imes using di e en genomic egions as ype.
This will be impossible o de ec wi hou a specimen om
which di e en genomic egions can be sequenced and
may con ibu e o he desc ip ion o unnecessa y new
names.
FINAL REMARKS
As discussed abo e, he e a e al e na i e ways o
communica ing he exis ence o axa only known om DNA
da a, which do no equi e modi ica ions o he ICN. Ins ead
o allowing DNA da a as ypes o axon names, da abase
egis a ion o candida e names can be used o pu a i e new
axa, when hei exis ence has been made plausible based
on a ious sou ces o in o ma ion (including bu no limi ed
o DNA sequences). A unc ional sys em o en i onmen al
sequences unde he Candida us o species hypo heses
app oach could esul om a ca e ully selec ed se o
equi emen s o ensu e high-quali y da a and ep oducibili y.
We submi ha p oposals F-005 and F-006, o he easons
ou lined he e, will no sol e he p oblems hey a e in ended
o sol e, dis ega d knowledge acqui ed h ough decades o
esea ch in he gene ics o specia ion, and will ins ead c ea e
con usion and subs an ial ex a wo k o con empo a y and
u u e mycologis s. We all ha e he esponsibili y o main ain
he scien i ic s anda ds o ep oducibili y as well as o p o ide
well-conside ed ules o coming gene a ions, so hey can
imp o e on ou wo k and ake app op ia e, well-in o med
axonomic decisions using all a ailable in o ma ion.
ACKNOWLEDGEMENTS
We wan o exp ess ou g a i ude o all people who en iched bo h he
ex and ou iews by gene ously sha ing hei opinions and scien i ic
expe ience.
Consequences o allowing sequence da a as ypes
ARTICLE
173
VOLUME 9 · NO. 1
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