DNA Barcoding and the biological species concept:
Valerio Sbordoni
Dipartimento di BiologiaUniversità di Roma “Tor Vergata”
‘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
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.
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
Mugil cephalus
Chelon labrosus
Liza aurata
Tapes decussatus
Tapes philippinarum
Species concepts according to Mayr (1969)
•Typological
•Nominalistic
•adimensional•Biological
•pluridimensional
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)
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)
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
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
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)
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
A necessary premise
We must distinguish DNA taxonomy from DNA barcoding, where the former directlyconcerns 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 45:1–10.
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, 262–277.
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.
136 bird species on Arfak Mountains (Irian Jaya)
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.
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.
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.
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?
Birds of North America 437 specimens, 263 species
Amphibia COI GenBank (89 species)
Cognato, (2006) Journal of Economic Entomology, 99:1037-1045
In summary:
DNA barcoding resolves most species, although some taxa have proved intractable
Waugh J (2007) BioEssays 29:188–197
Why?
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.)
Sympatric speciation in Rhagoletis pomonella
MitochondrialCOII sequences (687 nucleotides)
Smith and Bush.1997. Mol.Phyl.Evol.7:33–43
0.01 Genetic distance value
Allopatric speciation in Dolichopoda cave crickets
D.aegilion
D.baccettii
D.schiavazzii
Hybridization experiments in Dolichopoda: relationship between hatching rate and genetic distance
between parental populations and species
ORO
KAS
PAN
CHI
PUG
T.cavicola E.insolitus
H.cumberlandicus
CAMPST
FICMRC
ORS
CON
SAB
SAR
BRASIS
VLTD.bormansi D.cyrnensis
D.ligustica
D.laetitiae
D.geniculata
D.schiavazzii
D.muceddai
D.aegilion D.baccettii
D.palpata CPR
TRE
VAL
DIAPSC
GDPFONISC
SOLVEL
D.araneiformis
3
12
IZB12
POZ134
1
PER
2
12
12
1
43
2
KEF
12
DHAJOA2GLK
12 HER
ANA
ITA
SPI
AGH
ANT
NAU
EDE
DRA
1
PKIKSA
2TRI1
3
SPSEPT
SKA
KASDIR
KAT
1
12
2
NIKDHI
PAR23
D.sbordonii GOL
VOR D.euxina
D.linderi
D.capreensis
D.cassagnaui
D.dalensi
D.thasosensis
D.hussoni D.remyi
D.graeca D.pavesi
D.makrikapa
D.steriotisi
D.matsakisi
D.petrochilosi D.insignis
D.unicolor
D.paraskevi
D.vandeli
PNZ
Molecular phylogeny of the cave cricket genus Dolichopoda
Tree topology is congruent with the morphologically based taxonomy and clearly reflects a phylogeographic pattern
0.8<P<0.90.9<P<1.0
Allegrucci, Todisco & Sbordoni, 2005Mol. Phyl. Evol. 37: 53–164, and unpublished
KASb
DIR1
South
ern
Pelo
ponnesu
s
KAT1
TRI3 PAN
DHAJOA2
GLKHER2
South
-East
ern
Gre
ece
KSAPKI
3.13.4
SIS SAR
3.03.5
SOLVEL
EDEPOZ
IZBNAU
DRA1DRA2
ORO
ANT4AGH2
SPI2PERCH1
ITA2
SIR
CON PUG
VAL PNZ
DIAPSCISC
CAM
PST
FIC
MRC ORS
CPR
Western Mediterranean
TRE
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Alb
an
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Centr
al G
reece
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nia
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s.
KEF
ANA1KAS
Nort
hern
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s
SPSEPTSKA
East
ern
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ek Isl
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PAR3NIK2 DHI
Cre
te Is
landN
ort
hern
Gre
ece
KAR
GOL VOR
Turk
eyC
auca
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1.41.8
2.52.9
2.12.2
2.52.6
4.34.5
2.62.6 3.4
3.7
2.01.8
2.52.8 3.5
3.64.04.24.8
5.0 5.95.9
4.44.5
5.05.1
6.7 7.0
5.96.5
2.11.6
Genus Dolichopoda: 90 pop. samples, 33 species
1 30
25
50
75
100
015 17 19 22
25
50
75
100
25
50
75
100
5 10 150
Fre
quen
cy %
Divergence (%)
Within species Within genus Within family
Data from: Allegrucci, Todisco & Sbordoni, 2005. Mol. Phyl. Evol. 37: 53–164,
and unpublished
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.
P.p
hoeb
us
P.n
ord
man
P.c
lod
ius
5
1.01.0
1.01.0
1.01.0
P. mnemosyneP. mnemosyne
P. apolloP. apollo
P.a
riad
ne
P.ariad
ne
0.960.96
0.960.96
1.01.0
0.910.91
1.01.0
1.01.0
1.01.0
0.990.99
1.01.0
1.01.0
0.960.96
0.870.87
0.960.96
COI 869bpCOI 869bp50% MR Bayesian consensus50% MR Bayesian consensus
MrBayes (Huelsenbeck and Ronquist)MrBayes (Huelsenbeck and Ronquist)
Gratton, P., V.Todisco, and V.Sbordoni, in prepGratton, P., V.Todisco, and V.Sbordoni, in prep ..
Max D: 0.047Max D: 0.047
Max D: 0.024Max D: 0.024
How How manymany species in species in Parnassius?Parnassius?
COI, 931bp ML tree of 101 haplotypes
Parnassius mnemosyne
Gratton, P., Konopinski, M. & V.Sbordoni, in preparation
1.00
0.1
Parides vertumnusB. laos
0.98
0.971.00
1.00
0.590.62
1.00
1.00
1.00
1.00
1.00
1.00
0.98
0.63
1.00
1.00
1.00
0.89
0.97
1.000.52
1.00
1.00
0.98
1.00
B.crassipesB.demonius
B.daemoniusB.daemonius0.54
1.000.87
1.00
O.priamus euphorionTroides helena
1.00
B.p.pembertoniB.plutonius
B.plutoniusB.plutoniusB.plutonius
B.dasarada barataB.dasaradaB.dasaradaB.dasarada
B.d.barata
B.hedistus
B. alcinousB. a mansonensis
B. alcinous confusus
B.adamsoniiB.adamsonii
B.menciusB.mencius
B.polyeuctesB.polyeuctesB.p.polyeuctesB.p.polyeuctesB:p.lamaB.p.lamaB.p.lamaB.p.lama
B.polyeuctes
B.nevilliB.nevilliB.nevilli
B.latreillei Buthan
B.latreillei ButhanB.latreillei Buthan
B.latreillei India
B.latreillei Nepal
B.latreillei BirmaniaB.latreillei Birmania
B.latreillei Buthan
B.latreillei IndiaB.latreillei India
B.latreillei Himalaya
B.genestieri YunnanB.genestieri Yunnan
B.genestieri YunnanB.genestieri Yunnan
0.97
1.00
0.52
1.00
1.00
0.98
1.00
1.00
B.latreillei Bhutan
B.latreillei Bhutan
B.latreillei Bhutan
B.latreillei W Bengala
B.latreillei Nepal
B.latreillei Burma
B.latreillei
B.latreillei Bhutan
B.latreillei W Bengala
B.latreillei W Bengala
B.latreillei Him.Prad.
B.genestieri Yunnan
B.genestieri Yunnan
B.genestieri Yunnan
B.genestieri Yunnan
Burma
Byasa tree
Deodati T., D.Cesaroni & V.Sbordoni, in preparation
?
0.97
1.00
1.00
1.00
0.98
1.00
1.00
****
B.latreillei
B.l.genestieri
p=0.045
Byasa latreilleiByasa latreillei
Byasa genestieriByasa genestieri
0 0.02
0.04
0.06
0.08
0.1
0.12
0.14
0.16
0.17
0
50
100
150
200
250
300
350
400
450
N
Genetic distance
Within species Between Byasa species
Deodati T., D.Cesaroni & V.Sbordoni, in preparation
S. perspicillata(Savi, 1821)
S. terdigitata(Lacépède, 1788)
Genetic distance: 6.4%
Two Salamandrina cryptic species
Mattoccia M., A.Romano & V. Sbordoni Zootaxa 995: 1–19. (2005)
Photo: A.Romano
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.
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.
Ist
Bur Ine
Edr
Bay
Dem
KemOva
Bey
Olu
Sp
Sar
Kar
Kan
Cin
Go
OrtAkc
KayKur
Kor
EreBar
Inb AyaSin
Uny
GirMer
Hop
Geographic distance (km)
_ p(a
ve
ra
ge
freq
uen
cy o
f W
estern
allele
s)
Hop
Mer
Gir
Uny
Sin
AyaInb
Bar
Ere
Koc
Kur
Kay
AkcOrt
Kar
Sp1Sp2
Sp3
Kan
Sar
Go1
Go2
Go3
Cin
Ist
Ine
Bur
Dem
Edr
Bay
KemOva
Bey
Olu
0.0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1.0
-600 -400 -200 0 200 400 600 800 1000
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.
Castanea genotypes: Trees vs.seeds. Evidence of selection in the Anatolian
hybrid zone.
D.Cesaroni, F.Villani, A.Sansotta and V.Sbordoni, unpublished
Castanea genotypes: Trees vs.seeds. No apparent selection outside the
hybrid zone.
D.Cesaroni, F.Villani, A.Sansotta and V.Sbordoni, unpublished
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, 262–277.
A necessary word of warning
We must distinguish DNA taxonomy from DNA barcoding, where the former directlyconcerns 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 45:1–10.
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).
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.Sbordoni, 1993: Molecular Systematics and the Multidimensional Concept of Species. Biochem. Syst. Ecol.21:39-42
Fontaneto et al. (2007). PLoS Biol
A final homage to Alfred Russel Wallace for his farsighted ideas on species and speciation
Tanysiptera hydrocharis
Aru islands, N Guinea
Tanysiptera galatea
New Guinea
Ranges of Tanysiptera hydrocharis (H1 and H2) and T. galatea according to Mayr
Thanks for your attention