The second Linnaean revolution:
DNA sequencing and its impact on
traditional taxonomy
David Glenny1 and Murray Dawson2
Carl Linnaeus (1707–1778), the
father of modern taxonomy, would
never have conceived of DNA, let
alone the impact it would have on the
classification system that was named
in his honour.
number, but none of the data
traditionally collected by taxonomists
to help with classification gave
much certainty over evolutionary
relationships. DNA sequencing has
changed all this.
The Linnaean classification system,
also called the binomial system of
nomenclature, is still in use today.
It is a method of classifying living
organisms by combining a genus
name with a unique species name to
identify an organism. For example, the
scientific (binomial) name for humans
is Homo sapiens.
The development of the DNA
sequencing technique in the 1980s3
has made it possible to obtain what
are termed phylogenetic trees,
showing the evolution of organisms
going back hundreds of millions of
years. Increasing sophistication in
DNA sequencing technology and
the falling costs of sequencing now
make it practical for any taxonomist
to produce sequences for a group
of organisms, and then to fit these
into a larger data set obtainable from
GenBank, the international repository
for DNA sequences. A phylogenetic
tree constructed from DNA
sequences will show, with varying
degrees of certainty and resolution,
the evolutionary relationships of the
species sampled.
Traditionally, taxonomy was an
exercise in classification that used
mainly morphological features (size,
shape, colour, and many other
visible characters) to not only group
organisms into genera and species,
but also into families, orders, phyla, as
well as other intermediate ranks used
mainly by taxonomists themselves,
such as sections and subgenera,
subfamilies, suborders, etc.
Sometimes these morphological
features were supplemented by other
information such as chromosome
A
The impact of this on the taxonomy
of organisms in the last 20 years
has been considerable. Traditional
classifications are now being
B
C
Fig. 1 Monophyly, paraphyly, and polyphyly in phylogenetic trees: A, monophyletic groups
include alll the descendants of a particular species. It’s complete, and doesn’t contain any
species that are not descendants of that root ancestor species. A classification system
made up only of monophyletic genera is considered to be a desirable aim in taxonomy; B, a
paraphyletic group is one that is incomplete, i.e., it contains only some of the species that are
descendants of the root ancestor species; C, a polyphyletic group contains some or all of the
descendants, but not the common ancestor.
examined for their agreement with
phylogeny (the evolutionary history
of an organism). While in many
cases the traditional schemes are
in good agreement with DNA-based
phylogenies, in other cases they are
not.
The problem of paraphyly
One of the challenges for taxonomy
now is to translate a phylogeny
into a classification. Particularly
y The
vexing is the issue of paraphyly.
practice of representing evolutionary
relationships between species as
a tree diagram is relatively new,
and has highlighted a problem
in traditional classifications. A
p (Fig.1A) is a
monophyletic group
‘natural’ group or lineage that contains
all descendants of a single common
ancestor. A paraphyletic group
(Fig.1B) is one that contains only
some of the descendants, and so a
paraphyletic genus contains some
but not all species with a particular
ancestor4. When this situation
arises the excluded species are
usually transferred to another genus.
DNA sequencing shows that such
paraphyletic groups are extremely
common. At the moment there is a
lack of consensus among taxonomists
whether classifications should exclude
paraphyletic groups.
Hebe and Veronica
The most notable example of
DNA sequencing results revealing
paraphyly in the classification that
is relevant to New Zealand involves
the world-wide plant genus Veronica.
DNA sequencing carried out in
Europe, Australia and New Zealand
show that at present Veronica
a is a
paraphyletic genus. The species that
Landcare Research, PO Box 40, Lincoln 7640; [email protected];
[email protected]
3
See the previous article by Glenny et al. (pp. 8–9).
4
To further complicate matters, a third situation may occur where the group contains some or all of the descendants, but not the common
ancestor – this is called polyphyly (Fig. 1C).
1
2
New Zealand Garden Journal, 2008, Vol. 11(1) 11
are not included in Veronica
a are the
90 or so species in the New Zealand
genus Hebe.
Many New Zealanders regret the
idea that a name in common use
e might be dispensed with,
like Hebe
but phylogenetic taxonomists like
Professor Phil Garnock-Jones at
Victoria University believe that
classifications need to be aligned with
what we now know about evolutionary
relationships. Recently, GarnockJones and his colleagues published a
full set of formal combinations under
Veronica
a for the hebes (GarnockJones et al., 2007). These formal
combinations (species, subspecies,
varieties, etc.) mean that the names
under Veronica
a are now available for
use5.
Many taxonomists, in New Zealand
as well as overseas, have argued
strongly against making the many
changes that would result from this
realignment process, claiming it would
seriously destabilise classification
schemes now in place. They argue
that stability in names is a valuable
attribute of a classification that
makes it useful, particularly to nontaxonomists. Such taxonomists are
prepared to accept paraphyly in
classifications.
In the example above, evolutionary
taxonomists argue that it doesn’t
e within
make sense to nest Hebe
Veronica
a and give them both the rank
of genus. Two solutions are possible:
to combine all species into a single
large monophyletic genus, Veronica,
or to divide Veronica
a into numerous
monophyletic genera. Either way,
changes to the classification are
necessitated by alignment of a
classification with phylogeny.
Mike Bayly and Allison Kellow, in
their recent book An illustrated guide
to New Zealand Hebess (Bayly and
Kellow, 2006), discussed in detail the
pros and cons of adopting Veronica
as the genus for New Zealand hebes.
They argued that it might be best to
a into a number of smaller
split Veronica
genera, retaining Hebe
e as one of
them. They suggested that what are
currently subgenera within Veronica
(Fig. 2) could be regarded as genera
alongside Hebe.
Asparagaceae,
Asphodelaceae,
Asteliaceae,
Dracaenaceae,
Liliaceae, and
Lomandraceae.
DNA evidence has
concluded that
the correct family
for Cordyline
e is
Laxmanniaceae.
Arthropodium, the
rengarenga lily, has
also been included in
this family.
While the
Orchidaceae family
remains a natural
(monophyletic) group,
there have been
extensive changes
to the Australasian
orchids, particularly
Fig. 2 Phylogenetic tree showing the relationship of the Hebe
at the genus level
complex to Veronica. Reproduced with permission from Bayly
as a result of both
and Kellow (2006, fig. 6).
morphological and
Genus and family level changes to
DNA-sequencing work. For New
the New Zealand native flora
Zealand, these new names are
The Angiosperm Phylogeny Group
incorporated in the recently published
(APG) is a group of flowering plant
book Wild orchids of the lower North
taxonomists who aim to incorporate
Island
d (de Lange et al., 2007)7.
phylogenetic hypotheses derived from
However, the DNAsequencing work
DNA sequencing into an updated and
has not been fully published and many
practical classification system that
of the new names are not accepted by
follows the rules of the International
all taxonomists working in the family.
Code of Botanical Nomenclature6.
There have also been major changes
In 2003 they produced an overall
in
the Australasian epacrids. DNA
classification of the flowering plants.
phylogenies reject the southern
We have already outlined the genus
heath family Epacridaceae
level issues with Hebe
e and Veronica.
because it was nested within the
Following the APG classification (and
Ericaceae. As a consequence, the
the underlying studies that support it),
New Zealand genera Archeria,
Hebe, Veronica, and related genera
Dracophyllum, Epacris, Leucopogon,
(see list that follows) are now placed
and Pentachondra
a are now placed
in the Plantaginaceae family, rather
in a larger Ericaceae. In addition,
than Scrophulariaceae. Many other
molecular and morphological work
plant groups have been similarly
done in Australia on the epacrids
changed.
has led to major rearrangements in
the genera. New Zealand species
Cordyline
e is a well known genus,
were placed in Cyathodes
that
particularly because of the iconic
and
Leucopogon
n have now
and widely grown New Zealand
been
reassigned
to new genera
cabbage tree, C. australis. Perhaps
Androstoma,
Leptecophylla
a and
less well known is the long-standing
Acrothamnus.
This
work
is
incomplete,
uncertainty of which family to
as
Cyathodes
pumila,
Leucopogon
place this distinctive genus in.
fraserii and L. nanum
m have no place in
There are a multitude of earlier
the
new
generic
scheme.
placements including the Agavaceae,
Ironically, the first New Zealand hebes to be described were under the name Veronica, and it took many years for the horticultural trade to
accept the formal change to Hebe!
6
See http://www.mobot.org/MOBOT/research/APweb/welcome.html.
7
Reviewed in this issue (pp. 31–32).
5
New Zealand Garden Journal, 2008, Vol. 11(1) 12
Other changes affecting
g Ne
New
w
Zealan
nd na
ati
tive
ve gen
e er
era
a ar
a e:
Ac
A
can
anth
thaceae for Avicennia
a (rather
than Avicenniaceae);
Amaranthaceae for Atriplex,
x
Chenopodium, Einadia, Sarcocorni
niia,
and Suaeda
a (rather than
Chenopodiaceae);
Araceae for Lemn
mna and
mn
d Wolf
Wolfffifia
Wo
a
(rather than Lem
mn
na
a
ace
ceae
ce
ae);
ae
)
);
Argophyllace
eae
ae for
o Co
oro
oki
kia (ra
rath
her
er
than Escalloni
niiaccea
niac
eae or
or Co
orrokkia
acce
ea
ae
e);
Athero
r sp
s ermata
ace
cea
eae
ae for La
Laur
aur
u el
elia
eli
ia
(rat
(r
athe
herr th
than Mon
oniim
on
mia
ace
ea
ae
e);
);
Calceolariac
cea
eae for
o Jo
Jove
velllll ana
an
na (ra
rath
ath
ther
he
err
than
n Scrophu
hu
ula
ari
riac
acea
ae)
e);;
Celastrace
eae
e for
or Stac
Stac
St
ackhou
kkh
hou
o siia (rra
ath
her
e
than
th
an S
Sta
tack
ckho
houssia
ace
cea
ae
e));;
Hemerocallidac
ac
ce
ea
ae forr Di
Dia
anella
an
ellla
a
(rather than Pho
orm
miace
iacce
ia
eae
e),
),
Herpolirion
n (rather tha
an
Anthericaceae), Phormi
miiu
um
m (ra
atth
her
er
than Agavaceae, Phormiaceae,,
etc.), and Xeronema
a (rather than
Phormiaceae);
Hypericaceae for Hy
Hype
p ricu
pe
um (ra
rath
ther
e
th
than
han
n Clu
lusi
siac
iac
acea
eae));
Ixer
Ix
erba
bace
ceae
a for Ixxer
e ba
ba (ra
rath
ra
th
her ttha
ha
an
G os
Gr
ossu
sula
lariac
acea
eae
e or
o Bre
rexi
xiac
acea
eae)
e);;
Lamiac
Lami
acea
eae
e ffor
or Te
Teuc
u ri
uc
ridi
dium
um and Vi
um
V te
ex
(rat
(r
athe
he
er th
than
an
n Ver
erbe
bena
nacceae
na
ceae
ae);
)
M lv
Ma
vac
acea
ea
ae for
o Ente
En
ntele
te
ele
ea ((rra
rather
rath
th
her than
han
ha
Tilililiac
Ti
a ea
ac
eae)
e);;
e)
P ry
Ph
ryma
mace
ceae
ce
ae for
or Gl
Glos
osso
os
sost
so
stig
st
igma
ig
ma
a,
Mazzus
Ma
zus, an
and
d Mi
M mu
mulu
lus
lu
s (ra
ath
her
e tha
han
n
Scro
Sc
roph
ro
ph
hul
u ar
ariia
iace
ace
ea
ae
e);
)
Phyl
Ph
ylllant
ylla
ant
ntha
ha
hac
aceae
ceae
a for Or
Oreo
eopo
po
p
ora
rant
nthe
nt
hera
he
ra
and
an
d Po
Pora
rant
rant
nthe
hera
ra
a (ra
athe
th
he
err tha
an
Euph
Eu
phor
ph
o bi
or
b ac
acea
eae)
ea
e);;
e)
Plan
Pl
anta
an
tagi
ta
g na
gi
aceae
ce
eae for Ca
Callllllitititri
rich
ri
che
ch
e ((ra
rath
ra
th
her
than Cal
than
th
a lilitr
trric
cha
h ce
ceae
ae
e); Ch
C iono
io
ono
ohe
hebe
be,,
be
Grat
Gr
a io
at
i la
a, He
Helililioh
oheb
oh
e e, Le
eb
L on
onoh
oh
heb
be,
Limo
Li
mose
mo
selllllla
se
a, Ou
uri
r si
s a, Pa
Para
rahe
ra
hebe
he
be,,
be
Ve
V
ero
roni
n ca
ni
a [in
ncl
c ud
udin
in
ng he
ebe
bes]
s] ((ra
ra
ather
th
her
th
than
han
nS
Scr
crop
cr
ophu
op
phu
hula
la
arriiaccea
ae)); an
and
d
Plan
Pl
Plan
anta
ta
ago
g ;
P rt
Po
r ul
ulac
a ac
ac
a ea
eae
e for
or He
Hect
ctor
ct
orrel
o
ella
la
a (ra
r th
ther
er
th
han H
Hec
ecto
ecto
ec
t re
ellllac
a ea
ac
ae
e));
Qu
Q
uin
nti
tini
n ac
ni
acea
e e for Qu
ea
Q in
ntitin
nia ((ra
ni
nia
rath
ra
t er
th
than
th
han
an E
Essc
scal
a lo
oni
n ac
acea
eae
ea
e [p
[pos
osssi
ossi
s bl
bly]
y]);
y]);
R us
Ro
sse
eac
acea
ea
ae for
o Ca
Carp
rp
podet
odet
od
e us
s (ra
rath
ther
th
e
er
than
than
th
n Esccal
allo
loni
lo
nia
ni
acea
ac
ae)
e);;
Sa
ant
n al
a ac
ace
eae ffo
eae
ea
or Ko
or
K rttha
hals
hals
sella
ellla
a ((ra
ratth
ra
ther
er
than
th
an Visc
an
is
scace
cace
ca
ceae
ae);
ae);
Scro
Sc
roph
ph
hullar
a ia
iace
ceae
ce
ae
e for My
Myop
op
por
orum
um
(insstte
(i
(ins
ead
d of Myop
My
yop
por
orac
acea
ac
eae)
ea
e);;
e)
Theo
Th
e ph
eo
phra
ast
s ac
cea
e e forr Sa
S mo
m lu
luss
(rat
(r
athe
herr th
he
than
han
n Priimu
m la
ace
eae
a ).
)
Of course these changes and many
others will affect the placements
of the non-native cultivated and
naturalised flora as well, not only
in New Zealand but throughout the
world.
It is likely that most of these changes
will gain acceptance. Above all, these
changes are aimed at producing
a more natural (phylogenetic)
classification that reflects true
relationships between plant groups.
References
Bayly, M. and Kellow, A.V. (2006).
An illustrated guide to New
Zealand Hebes. Te Papa Press,
Wellington.
Cantino, P.D. and de Queiroz, K.
(2007). International Code of
Phylogenetic Nomenclature.
Accessed at http://www.ohiou.
edu/phylocode/ on 22 May 2008.
de Lange, P.; Rolfe, J.; St George,
I.; Sawyer, J. (2007). Wild
orchids of the lower North
Island: field guide. Department
of Conservation, Wellington
Conservancy.
Garnock-Jones, P.; Albach, D.;
Briggs, B.G. (2007). Botanical
names in Southern Hemisphere
Veronica
a (Plantaginaceae):
sect. Detzneria, sect. Hebe, and
sect. Labiatoides. Taxon 56(2):
571–582.
Wikipedia (2008a). Nomenclature
codes. Accessed at http://
en.wikipedia.org/wiki/
Nomenclature_Codes on 22 May
2008.
Wikipedia (2008b). Phylocode.
Accessed at http://en.wikipedia.
org/wiki/PhyloCode on 22 May
2008.
In
nte
t rn
nat
a io
ona
nall Co
Code
des
de
s of
N me
No
menc
n la
nc
atu
t re
Zool
Zo
olog
olog
o ic
cal
al,, Bo
Bota
ota
tani
nica
ni
cca
al,, a
and
nd Bacte
acte
ac
eri
r al
a
c de
co
d s (W
Wik
ikip
iped
ip
edia
edia
a, 20
008
08a)
8a) h
hav
avve
d ve
de
v lo
lope
ope
ped
d sinc
sinc
si
nce
e th
the
e tit me
m of Li
L nnae
nn
nae
eus
us,
and
an
d ar
a e am
men
ende
de
ed by
by int
nter
errna
natition
on
onal
nal
gath
ga
th
ther
her
erin
ings
in
gs of ta
axo
x no
n mi
mist
sstts. The
Bota
Bo
tani
nica
call Co
ca
C de
d of No
Nome
menc
ncla
atu
ture
re is
a en
am
e de
d d byy bot
o an
nic
ical
al ccon
al
ongr
on
gres
gr
e se
es
es
t at mee
th
e t evve
erry fo
f ur
u yea
ears
rs,, an
rs
nd
be
eca
c us
u e th
t en
nu
umb
mber
mber
erss off ttax
axxon
a
onom
onom
omiis
ists
s
atte
atte
at
tend
n in
nd
ing
g th
the
esse co
e
ong
gress
rre
ess
sses
ses a
are
re lar
re
arge
ge
e
and
an
d vo
otit ng rig
igh
htts ar
are
e he
h ld
d by al
all,l, it is
virt
vi
rtua
rt
uallllllyy im
ua
mpo
poss
ssib
ss
ib
ble
e to ga
g in
i maj
ajor
jor
oritityy
supp
su
ppor
pp
ortt fo
or
forr any
an
ny ra
r di
dica
c l am
ca
amen
endm
en
dm
men
entss.
The Ph
T
Phyl
yloC
oCod
ode
e
A nu
numb
mb
ber of ev
evol
olut
utio
iona
nary
y taxon
onom
mis
ists
t
have proposed a PhyloC
Code (Canti
C tino
no
and de Queiroz, 2007), a set of
rules in which no rank is asssi
sign
g ed
to names above spe
pecies
es
s level. At
present the
e ra
rank
n s of gen
nk
nus
us and familly
a e compullso
ar
sorry, mean
nin
ing
g th
that every
species
sp
p
must be as
assi
signe
ed tto
ed
o a ge
g nu
nus
and
an
nd family. Und
der the Phyl
yloC
oCod
o e, onl
od
onlyy
s ec
sp
ecies rank wo
ould
ld b
be
e co
com
mpulso
mpul
so
ory
r ,
an
a
nd genus and famiily rran
a ks would
diisa
d
isa
appea
pp
pe r. There would still be a
he
hi
erra
arrch
chy in the
en
nam
ames, but there
woul
wo
uld be
be m
more
e flexibililitity ov
over
er w
wha
hatt
gro
gr
rou
oup
pss werre re
eco
cognised.
In the
the
h cas
ase
e off Ver
Vero
Ve
roni
n ca
a and Hebe, the
flflex
exxibil
e
ib
bililit
litity o
ovve
err namin
ng would me
ean
that b
th
bot
oth
ot
h Ve
eron
roni
ro
nica
a and He
H be
be could
co
cont
ont
ntin
in
nu
ue
e to be
e usse
ed,
d and a hierarchy
wo
w
oul
oul
u d be
be pro
ovi
vd
de
ed that would show
that
th
at H
He
ebe
be is ne
nest
stted
ed within Veronica.
Th
T
he ma
main
i obsttacle to the PhyloCode
b coming popular is the loss of
be
the binomial naming system that
has its origin with Linnaeus. Hebe
suba
su
balp
lp
pin
ina
a iiss th
he bi
b no
omi
m al
a for a
comm
co
comm
mmon
mo
on
n New
w Zea
eal
aland
land
la
d sspe
pe
eci
cies
cies
s, in
n
whic
wh
ich
ic
ch th
the
e fifirs
rstt na
rs
name
me is sh
har
ared with
ared
h
a l ot
al
othe
herr h
he
he
ebe
bes,
s, b
but
ut tthe
he ssec
econ
ec
ond
d na
name
me
e
q al
qu
a ifi
fie
ess itt u
uni
niiqu
quel
e y: the
el
here
re is on
only
ly
y one
e
ssp
peccies wi
pec
with
th that
ha
at bi
bino
nomi
miial
a . Un
Unde
de
er
the
th
e Ph
Phyl
y oC
yl
oCod
de,
e the
here
r wou
re
ould
uld b
be
e no
no
fifixe
xe
ed ra
ank of ge
g nu
n s wi
with
t the
th
he res
esul
ultt
ul
th
that
hat the
he fam
fam
amililia
iarr bi
bino
nomi
no
m al
mi
a sys
y te
tem
m
woul
wo
uld
d be d
dis
i co
is
cont
ntin
in
nue
ed. N
No
o go
good
od
a te
al
tern
rn
nat
a ive
iv
ve in
nvolv
vo
olv
lvin
ing
ng th
he su
ubsstit tu
t tition
on of
of
unin
un
in
nomia
omials h
om
has
a bee
as
een
n pu
p t fo
orw
war
a d.
d
As W
As
Wik
ikip
ik
kip
i e
ed
dia
a ((20
2008
20
08b)
08
b) say
ays,
s, “Th
he
Phyl
Ph
y oC
yl
oCod
od
de is
i ccon
ontr
on
trovver
trov
tr
e si
sial
al.
al
l. Th
The
e
numb
nu
mber
mb
e of su
er
supp
ppor
pp
orte
or
ters
te
rs
s for
o o
offi
ffificial
ia
al
adop
ad
optitition
op
on
n of th
the
e Ph
P yl
yloC
Cod
de is
s stit llll
smal
sm
alll,l, and
al
nd iitt is
i u
unc
nccer
ncer
erta
tain
in,, as o
off 20
2007
07
7,
when
wh
en the
e cod
ode
e will
willl b
be
e impl
im
mpl
p em
men
ente
te
ed
and
an
d ho
ow wi
w de
dely
ly iitt wi
ly
willll be fo
follllllow
ow
wed
e .”
An
nu
umb
mber
er of ta
taxo
xo
ono
n mi
mist
sstts ha
ave
begu
be
gu
g
un tto
o pub
ubllish
lish
s nam
ames
mess und
nder
err tthe
e
he
e
P yl
Ph
y oC
Cod
de
e,, and
d whi
hile
le
e the
h se
e names
am
mess
don’
do
n’’t ha
n’t
havve
ve officia
iall st
stan
a di
an
ding
ing
ng und
nder
nder
e the
exis
ex
is
stiting
ng
g cod
odes
es of no
nome
m nc
me
cla
atu
ture
re
e, th
they
ey
prres
p
esen
en
ent
nt a ch
chal
alle
al
le
eng
ge to
t ort
r ho
hod
doxy
do
xy:: if
enou
en
ough
ou
gh
g
h tax
a on
nom
mis
ists
ts pub
blilish
lish in th
his
s
wa
w
ay an
a d th
t eyy are adopt
do
opt
pe
ed
d by ot
o he
h rs
rs,,
th
heyy willl ga
ain
nd
de
e fact
fa
act
cto
o stan
sta
st
an
ndi
ding
ng..
New Zealand Garden Journal, 2008, Vol. 11(1) 13