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DNA Barcoding and the biological species
concept Valerio Sbordoni Dipartimento di
Biologia Università di Roma Tor Vergata
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The species concept is one of the oldest and
most fundamental in biology. And yet it is almost
universally conceded that no satisfactory
definition of what constitutes a species has ever
been proposed. Th. Dobzhansky (1935). A
Critique of the Species Concept in Biology.
Philosophy of Science, 2 344-355
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Who needs species? An accurate definition of
species has become a requirement not only within
the frame of systematics but also in all those
fields relevant to conservation, food, health,
trade and the ensuing laws.
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In the unavoidable progress of taxonomy and
nomenclatural changes, we face such paradoxes as
that of the recognition of a species status for
an endemic organism, which brings as a
consequence its bureaucratic cancellation from a
conservation red list (e.g. Bombina variegata-
B.pachypus problem in the Habitat
Directive) It is therefore necessary to
outline operational, clear-cut rules for the
delimitation of species.
Bombina variegata
Bombina pachypus
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Mugil cephalus
Chelon labrosus
Liza aurata
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• Species concepts according to Mayr (1969)
• Typological
• Nominalistic
• adimensional
• Biological
• pluridimensional

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The Nominalistic Species Concept From this
remarks it will be seen that I look at the term
species as one arbitrarily given, for the sake of
convenience, to a set of individuals closely
resembling each other, and that it does not
essentially differ from the term variety, which
is given to less distinct and more fluctuating
forms. The term variety, again, in comparison
with mere individual differences, is also applied
arbitrarily, for convenience sake. (C.Darwin,
1859)
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Biological species concept related definitions
I "No matter what variations occur in the
individuals or the species, if they spring from
the seed of one and the same plant, they are
accidental variations and not such as to
distinguish a species permanently one species
never springs from the seed of another nor
viceversa. (Ray, 1686)
John Ray (1627-1705)
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Biological species concept related definitions
II un ensemble ou une collection d'individus
semblables ou presque semblables, qui furent
produits par d'autres individus pareils à eux
(J.B.Lamarck, 1803)
Jean Baptiste de Lamarck 1744-1829
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Biological species concept related definitions
III a whole of individual organisms resembling
each other more than they resemble to any other
individual organism, that are able, by
interfertility, to reproduce fertile individuals
who reproduce themselves in the same way, so that
by analogy one could assume that they all are
originated by a single individual organism. (De
Candolle, 1813)
Augustin Pyramus de CANDOLLE 1778 - 1841
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Biological species concept related definitions
IV-VI "a genetic species is a group of organisms
so constituted and so situated in nature that a
hereditary character of anyone of these organisms
may be transmitted to a descendant of any other
(Simpson,1943) "...the largest and most inclusive
...reproductive community of sexual and
cross-fertilizing individuals which share in a
common gene pool" (Dobzhansky,1950) "groups of
actually or potentially interbreeding natural
populations which are reproductively isolated
from other such groups" (Mayr,1940)
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Phenetic concept Michener,1970, Sneath Sokal,
1973, Nelson Platnick,1981 Recognition
concept Paterson,1978 Ecological concept Van
Valen, 1976, Mayr, 1982 Evolutionary concept
Simpson,1961, Wiley,1978, etc. Phylogenetic
concept deQuieroz and Donoghue, 1990 Phenetic
concept Michener,1970, Sneath Sokal, 1973,
Nelson Platnick,1981 Economical concept
Ghiselin,1974 Cohesion concept Templeton, 1989
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A necessary premise We must distinguish DNA
taxonomy from DNA barcoding, where the former
directly concerns the circumscription and
delineation of species using evolutionary species
concepts and the latter is a means of identifying
a priori entities by sequence similarity Vogler
AP, Monaghan MT (2007) J Zool Syst Evol Res
45110.
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The actual demarcation of species taxa uses
morphological, geographical, ecological,
behavioral, and molecular information to infer
the rank of isolated populations. Mayr, E.
(1995) Philos. Sci. 63, 262277.
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Do species exist in nature? Objectivity
vs.conventionalism In an adimensional
perspective, in sexual organisms effectively or
potentially amphigonic (including geographic,
facultative parthenogenesis, etc.), species exist
since they are recognized, as potential mates, by
organisms themselves.
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136 bird species on Arfak Mountains (Irian Jaya)
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Species can, at times, be predicted The Malgasy
Orchid Angraecum sesquipedale Thouars and its
pronube the sphingid moth Xanthopan morgani
praedicta Rothschild Jordan. Based on the
exceptional depth of the Orchid nectaria, this
moth, first imagined by Darwin in1862, and
painted by Wallace in 1864, was effectively
discovered 40 years later.
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Do species exist in nature? Objectivity
vs.conventionalism In an adimensional
perspective, in sexual organisms effectively or
potentially amphigonic (including geographic,
facultative parthenogenesis, etc.), species exist
since they are recognized, as potential mates, by
organisms themselves. The problems arise when
considering species in a pluridimensional
perspective. Moreover nobody would think that
first RNA organisms, supposedly the originators
of life, were organized in species, and similar
situations can be expected to occur in other
living beings.
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Some critical views 1 Reality of species is now
doubted by many. 2 Reproductive isolation is no
longer generally recognized as the best
definition of species. 3 Speciation does not
require allopatry. 4 Natural selection is
becoming viewed as the primary cause of
speciation.?? Coyne, J.A. 1994. Evolution 48
19-30. Mallet, J. 2001. J .Evol. Biol. 14
887-888.
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• Detecting species from DNA sequences

DNA sequencing, with key sequences serving as a
"barcode", has been proposed as a technology that
might speed up species identification. How this
approach performs in different kinds of species?
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Birds of North America 437 specimens, 263 species
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Amphibia COI GenBank (89 species)
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Cognato, (2006) Journal of Economic Entomology,
991037-1045
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In summary DNA barcoding resolves most species,
although some taxa have proved intractable
Waugh J (2007) BioEssays 29188197 Why?
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• Species reflect, in their properties, the mark of
  speciation, where the following factors have more
  or less predominant roles
• The genetic system (polyploid speciation,
  stasipatric speciation, inversion polymorphism
  speciation, etc.)
• Natural selection promoting niche shift
  (sympatric speciation)
• Evolutionary time leading to divergent mutation
  accumulation (allopatric, peripatric speciation,
  etc.)

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Sympatric speciation in Rhagoletis pomonella
Mitochondrial COII sequences (687
nucleotides) Smith and Bush.1997.
Mol.Phyl.Evol.73343
0.01 Genetic distance value
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Allopatric speciation in Dolichopoda cave
crickets
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Hybridization experiments in Dolichopoda
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Hybridization experiments in Dolichopoda
relationship between hatching rate and genetic
distance between parental populations and species
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Molecular phylogeny of the cave cricket genus
Dolichopoda
Tree topology is congruent with the
morphologically based taxonomy and clearly
reflects a phylogeographic pattern
Allegrucci, Todisco Sbordoni, 2005 Mol. Phyl.
Evol. 37 53164, and unpublished
0.80.9 33
Western Mediterranean
ORS
MRC
Central Greece/ Ionian Isls.
FIC
CAM
SAR
SIS
Northern Greece
South-Eastern Greece
Southern Peloponnesus
VAL
PST
VLT
Northern Peloponnesus
PNZ
ISC
TRE
CPR
PSC
DIA
2.1 1.6
Eastern Greek Isls.
CH1
SPI2
ITA2
PER
Albany
2.1 2.2
1.4 1.8
ANT4
PUG
CON
AGH2
IZB
Crete Island
EDE
JOA2
NAU
KAS
2.0 1.8
KSA
2.5 2.6
POZ
DHA
ANA1
PKI
DRA2
PAN
KEF
DRA1
TRI3
2.5 2.9
HER2
DIR1
2.6 2.6
SIR
GLK
VEL
KAT1
SOL
ORO
2.5 2.8
3.0 3.5
3.1 3.4
KASb
3.4 3.7
3.5 3.6
SKA
EPT
SPS
DHI
NIK2
4.4 4.5
4.3 4.5
Caucasus
4.0 4.2
PAR3
4.8 5.0
5.0 5.1
5.9 5.9
GOL
Turkey
VOR
5.9 6.5
KAR
6.7 7.0
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Genus Dolichopoda 90 pop. samples, 33 species
100
100
75
75
50
50
25
25
0
0
1
3
15
17
19
22
Data from Allegrucci, Todisco Sbordoni, 2005.
Mol. Phyl. Evol. 37 53164, and unpublished
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Species are the result of historical processes,
such as population changes in demography,
geographical location and range extent, and
eventually speciation. Phylogeographical
analysis is therefore of great help to inferring
these stories and understanding the real meaning
of species.
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P. apollo
Max D 0.047
P.phoebus
P.ariadne
P.ariadne
1.0
1.0
Max D 0.024
P.clodius
How many species in Parnassius?
COI 869bp 50 MR Bayesian consensus MrBayes
(Huelsenbeck and Ronquist) Gratton, P.,
V.Todisco, and V.Sbordoni, in prep.
P. mnemosyne
P.nordman
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COI, 931bp ML tree of 101 haplotypes
Parnassius mnemosyne
Gratton, P., Konopinski, M. V.Sbordoni, in
preparation
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Byasa tree
Deodati T., D.Cesaroni V.Sbordoni, in
preparation
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B.latreillei
p0.045
B.l.genestieri
?
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450
400
350
300
250
N
200
150
100
50
0
0
0.1
0.02
0.04
0.06
0.08
0.12
0.14
0.16
0.17
Deodati T., D.Cesaroni V.Sbordoni, in
preparation
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Two Salamandrina cryptic species
Mattoccia M., A.Romano V. Sbordoni Zootaxa
995 119. (2005)
S. perspicillata (Savi, 1821)
Photo A.Romano
Genetic distance 6.4
S. terdigitata (Lacépède, 1788)
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The Italian Peninsula in the Pliocene Black
circles sampling sites of Salamandrina
perspicillata. Black stars sampling sites of
Salamandrina terdigitata. Sites where haplotypes
of both clades have been found are reported as a
star inside a black circle. M. Mattoccia,
A.Romano and V. Sbordoni, in prep.
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The role of hybrid zones Rather then
representing a confusing issue, secondary
contact, hybrid zones stand for a great tool for
the delimitation of species. In fact they
contribute to the solution of the conflict
between adimensional and polytypic species.
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Villani, F., A.Sansotta, M.Cherubini, D.Cesaroni
and V.Sbordoni. 1999. Genetic structure of
natural populations of Castanea sativa in Turkey
evidence of a hybrid zone. J. Evol. Biol., 12
233-244.
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Castanea genotypes Trees vs.seeds. Evidence of
selection in the Anatolian hybrid
zone. D.Cesaroni, F.Villani, A.Sansotta and
V.Sbordoni, unpublished
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Castanea genotypes Trees vs.seeds. No apparent
selection outside the hybrid zone. D.Cesaroni,
F.Villani, A.Sansotta and V.Sbordoni, unpublished
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Towards an operational approach The actual
demarcation of species taxa uses morphological,
geographical, ecological, behavioral, and
molecular information to infer the rank of
isolated populations. Mayr, E. (1995) Philos.
Sci. 63, 262277.
48
A necessary word of warning We must distinguish
DNA taxonomy from DNA barcoding, where the former
directly concerns the circumscription and
delineation of species using evolutionary species
concepts and the latter is a means of identifying
a priori entities by sequence similarity Vogler
AP, Monaghan MT (2007) J Zool Syst Evol Res
45110.
49
Towards an operational approach An
irreducible basal cluster of organisms
diagnostically different from other such clusters
and within which there is a parental pattern of
descent - applies to both asexual and sexual
organisms (deQuieroz and Donoghue, 1990).
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Towards an operational approach Species are
seen as groups of individuals which are
discretely separated from other such groups in
the space defined by their descriptors V.Sbordo
ni, 1993 Molecular Systematics and the
Multidimensional Concept of Species. Biochem.
Syst. Ecol.2139-42
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Fontaneto et al. (2007). PLoS Biol
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A final homage to Alfred Russel Wallace for his
farsighted ideas on species and speciation
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Tanysiptera hydrocharis Aru islands, N Guinea
Tanysiptera galatea New Guinea
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Ranges of Tanysiptera hydrocharis (H1 and H2) and
T. galatea according to Mayr
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Thanks for your attention