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DNA Barcoding and the biological species concept: Valerio Sbordoni Dipartimento di Biologia

DNA Barcoding and the biological species concept: Valerio Sbordoni Dipartimento di Biologia Università di Roma “Tor Vergata”.

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DNA Barcoding and the biological species concept: Valerio Sbordoni Dipartimento di Biologia

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  1. DNA Barcoding and the biological species concept: Valerio Sbordoni Dipartimento di Biologia Università di Roma “Tor Vergata”

  2. ‘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

  3. 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.

  4. 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

  5. Mugil cephalus Chelon labrosus Liza aurata

  6. Tapes decussatus Tapes philippinarum

  7. Species concepts according to Mayr (1969) • Typological • Nominalistic • adimensional • Biological • pluridimensional

  8. 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)

  9. 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)

  10. 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

  11. 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

  12. 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)

  13. 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

  14. 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 45:1–10.

  15. 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.

  16. 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.

  17. 136 bird species on Arfak Mountains (Irian Jaya)

  18. 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.

  19. 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.

  20. 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.

  21. 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? Detecting species from DNA sequences

  22. Birds of North America 437 specimens, 263 species

  23. Amphibia COI GenBank (89 species)

  24. Cognato, (2006) Journal of Economic Entomology, 99:1037-1045

  25. In summary: DNA barcoding resolves most species, although some taxa have proved intractable Waugh J (2007) BioEssays 29:188–197 Why?

  26. 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.)

  27. Sympatric speciation in Rhagoletis pomonella Mitochondrial COII sequences (687 nucleotides) Smith and Bush.1997. Mol.Phyl.Evol.7:33–43 0.01 Genetic distance value

  28. Allopatric speciation in Dolichopoda cave crickets

  29. D.schiavazzii D.baccettii D.aegilion

  30. Hybridization experiments in Dolichopoda: relationship between hatching rate and genetic distance between parental populations and species

  31. T.cavicola E.insolitus H.cumberlandicus D.linderi D.ligustica CON D.aegilion PUG CAM D.baccettii PST FIC D.schiavazzii MRC ORS D.cyrnensis SAB VLT D.bormansi BRA SIS D.muceddai SAR D.capreensis CPR D.palpata TRE D.laetitiae DIA PSC GDP D.geniculata FON ISC VAL PNZ D.araneiformis SOL VEL D.thasosensis 1 DRA 2 4 EDE D.remyi 3 1 POZ D.hussoni 2 NAU 1 3 IZB D.steriotisi 4 ANT 3 2 AGH 1 1 ITA 2 2 CHI D.pavesi 1 2 SPI D.graeca 1 PER ORO ANA D.matsakisi 1 2 D.dalensi KAS KEF D.vandeli 2 HER 1 GLK D.petrochilosi 2 JOA 1 D.insignis DHA PAN PKI D.makrikapa KSA D.cassagnaui 2 TRI 1 3 KAS 1 D.unicolor DIR 2 1 KAT 2 SPS EPT SKA NIK DHI D.paraskevi 2 PAR D.euxina 3 GOL VOR D.sbordonii 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: 53–164, and unpublished 0.8<P<0.9 0.9<P<1.0

  32. 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 2.0 1.8 KAS 2.5 2.6 KSA POZ ANA1 DHA PKI DRA2 PAN KEF DRA1 TRI3 2.5 2.9 HER2 DIR1 2.6 2.6 SIR GLK VEL SOL KAT1 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 4.4 4.5 NIK2 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

  33. Within species Within genus Within family 100 75 Frequency % 50 25 Divergence (%) 0 5 10 15 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: 53–164, and unpublished

  34. 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.

  35. 0.96 0.96 0.91 1.0 1.0 1.0 0.96 1.0 1.0 0.99 0.96 1.0 0.87 1.0 1.0 5 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

  36. COI, 931bp ML tree of 101 haplotypes Parnassius mnemosyne Gratton, P., Konopinski, M. & V.Sbordoni, in preparation

  37. Parides vertumnus B. laos B.p.pembertoni 1.00 B.plutonius 1.00 B.plutonius 0.97 B.plutonius 0.98 B.plutonius 1.00 B.dasarada barata 1.00 B.dasarada B.dasarada 0.62 B.dasarada 0.59 B.d.barata 1.00 B.latreillei W Bengala B. a mansonensis B. alcinous 1.00 B. alcinous confusus B.latreillei W Bengala B.hedistus 0.98 B.adamsonii 1.00 B.latreillei W Bengala B.adamsonii B.mencius 0.97 B.latreillei Bhutan 1.00 1.00 B.mencius B.polyeuctes B.latreillei Bhutan B.polyeuctes B.p.polyeuctes 1.00 B.latreillei Bhutan B.p.polyeuctes 1.00 B:p .lama 0.89 B.latreillei Bhutan B.p.lama 0.63 B.p.lama B.p.lama B.polyeuctes B.latreillei Nepal 1.00 B.nevilli 1.00 B.nevilli B.latreillei Him.Prad. 1.00 B.nevilli 0.52 B.latreillei India B.latreillei Burma B.latreillei India 1.00 B.latreillei India B.latreillei Burma 0.97 B.latreillei Buthan 1.00 B.latreillei Buthan B.genestieri Yunnan B.latreillei Buthan 1.00 1.00 B.latreillei Buthan B.genestieri Yunnan B.latreillei Nepal 1.00 B.latreillei Himalaya B.genestieri Yunnan 1.00 B.latreillei Birmania 0.52 0.98 1.00 B.latreillei Birmania B.genestieri Yunnan B.genestieri Yunnan B.genestieri Yunnan 1.00 B.genestieri Yunnan 0.98 B.genestieri Yunnan B.crassipes 0.87 B.demonius 1.00 B.daemonius 0.54 B.daemonius O .priamus euphorion 1.00 Troides helena 0.1 Byasa tree Deodati T., D.Cesaroni & V.Sbordoni, in preparation

  38. 0.97 1.00 1.00 1.00 1.00 * * 1.00 * * 0.98 Byasa latreillei Byasa genestieri B.latreillei p=0.045 B.l.genestieri ?

  39. Between Byasa species Within species Genetic distance 450 400 350 300 N 250 200 150 100 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

  40. Two Salamandrina cryptic species Mattoccia M., A.Romano & V. Sbordoni Zootaxa 995: 1–19. (2005) S. perspicillata (Savi, 1821) Photo: A.Romano Genetic distance: 6.4% S. terdigitata (Lacépède, 1788)

  41. The Italian Peninsula in the Pliocene Black circles: sampling sites of Salamandrinaperspicillata. Black stars: sampling sites of Salamandrinaterdigitata. 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.

  42. 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.

  43. 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.

  44. Castanea genotypes: Trees vs.seeds. Evidence of selection in the Anatolian hybrid zone. D.Cesaroni, F.Villani, A.Sansotta and V.Sbordoni, unpublished

  45. Castanea genotypes: Trees vs.seeds. No apparent selection outside the hybrid zone. D.Cesaroni, F.Villani, A.Sansotta and V.Sbordoni, unpublished

  46. 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.

  47. 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 45:1–10.

  48. 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).

  49. 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

  50. Fontaneto et al. (2007). PLoS Biol

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