G. Gandolfi, P. S.-zerunian, &. Torricelli, and . Marconato, , 1991.

M. Dell'ambiente, Instituto Poligrafico e Zecca dello Stato, Rome, p.616

J. García-marín, F. M. Utter, and &. Pla, Postglacial colonization of brown trout in Europe based 677 on distribution of allozyme variants, Heredity, vol.82, pp.46-56, 1999.

S. T. Garnett and &. L. Christidis, Taxonomy anarchy hampers conservation -The classification of 679 complex organisms is in chaos, Nature, vol.546, pp.25-27, 2017.

A. &. Gauthier and . Berrebi, La colonisation de l'île par différentes souches de truite. Guide de gestion 681 de la truite macrostigma, pp.4-10, 2007.

E. Giuffra, L. Bernatchez, and &. Guyomard, Mitochondrial control region and protein coding genes 683 sequence variation among phenotypic forms of brown trout Salmo trutta from northern Italy, 1994.

, Molecular Ecology, vol.3, pp.161-171

E. Giuffra, R. Guyomard, and &. Forneris, Phylogenetic relationships and introgression patterns 686 between incipient parapatric species of Italian brown trout (Salmo trutta L. complex), Molecular 687 Ecology, vol.5, pp.207-220, 1996.

P. Gratton, G. Allegrucci, V. Sbordoni, and G. A. , The evolutionary jigsaw puzzle of the 689 surviving trout (Salmo trutta L. complex) diversity in the Italian region. A multilocus Bayesian 690 approach, Molecular Phylogenetics and Evolution, vol.79, pp.292-304, 2014.

R. Guyomard, Diversité génétique de la truite commune, 1989.

, Pisciculture, vol.314, pp.118-135

K. E. Hamilton, A. Ferguson, J. B. Taggart, T. Tomasson, A. Walker et al., Post-glacial 694 colonisation of brown trout, Salmo trutta L.: Ldh-5 as a phylogeographic marker locus, Journal, p.695, 1989.

, Fish Biology, vol.35, pp.651-664

P. D. Hebert, A. Cywinska, S. L. Ball, and &. R. Dewaard, Biological identifications through DNA 697 barcodes, Proceedings of the Royal Society, Ser. B, Biological Sciences, vol.270, pp.313-321, 2003.

L. E. Holm and . Bendixen, Oncorhynchus mykiss clone TAA72-13, sequence tagged site, p.699, 2000.

N. J. Isaac, J. Mallet, and G. M. Mace, Taxonomic inflation: its influence on macroecology and 701 conservation, Trends in Ecology and Evolution, vol.19, pp.464-469, 2004.

O. R. Jones and J. I. Wang, COLONY: a program for parentage and sibship inference from 703 multilocus genotype data, Molecular Ecology Resources, vol.10, pp.551-555, 2010.

L. L. Knowles and . Carstens, Delimiting species without monophyletic gene trees, Systematic, vol.705, issue.6, pp.887-895, 2007.

M. Kottelat, European freshwater fishes. An heuristic checklist of the freshwater fishes of Europe 707 (exclusive of former USSR), with an introduction for non-systematists and comments on 708 nomenclature and conservation, Biologia, Bratislava, vol.52, pp.1-271, 1997.

M. &. Kottelat and . Freyhof, Handbook of European freshwater fishes, Publications Kottelat, p.710, 2007.

. Ch-&-freyhof, , vol.646

C. R. Largiadèr and . Scholl, Genetic introgression between native and introduced brown trout 712 (Salmo trutta L.) populations in the Rhone River Basin, Molecular Ecology, vol.5, pp.417-426, 1996.

L. Lucentini, A. Palomba, L. Gigliarelli, H. Lancioni, P. Viali et al., Genetic 714 characterization of a putative indigenous brown trout (Salmo trutta fario) population in a secondary 715 stream of the Nera River Basin (Central Italy) assessed by means of three molecular markers, Italian 716 Journal of Zoology, vol.73, pp.263-273, 2006.

S. Mari?, S. Bajec, J. Schöffmann, V. Kostov, and &. Snoj, Phylogeography of stream-718 dwelling trout in the Republic of Macedonia and a molecular genetic basis for revision of the 719 taxonomy proposed by S. Karaman, Hydrobiologia, vol.785, pp.249-260, 2017.

O. M. Mcmeel, E. M. Hoey, and &. A. Ferguson, Partial nucleotide sequences, and routine typing by 721 polymerase chain reaction-restriction fragment length polymorphism, of the brown trout (Salmo 722 trutta) lactate dehydrogenase, LDH-C1*90 and *100 alleles, Molecular Ecology, vol.10, pp.29-34, 2001.

P. Massidda, Salmo (trutta) macrostigma in Sardegna, Biologia Ambientale, vol.5, pp.40-43, 1995.

F. Orrù, A. M. Deiana, and &. Cau, Introduction and distribution of alien freshwater fishes on the 750 island of Sardinia (Italy): an assessment on the basis of existing data sources, Journal of Applied, p.751, 2010.

, Ichthyology, vol.26, issue.2, pp.46-52

T. Patarnello, L. Bargelloni, F. Caldara, and &. Colombo, Cytochrome b and 16S rRNA sequence 753 variation in the Salmo trutta (Salmonidae, Teleostei) species complex, Molecular Phylogenetics and 754 Evolution, vol.3, pp.69-74, 1994.

A. B. Phillimore and I. P. Owens, Are subspecies useful in evolutionary and conservation biology?, 756 Proceedings of the Royal Society of London, Series B, vol.273, pp.1049-1053, 2006.

F. P. Pomini, Ricerche sul Salmo macrostigma Dum. Bollettino di Pesca, p.758, 1940.

, Idrobiologia, vol.16, issue.3, pp.12-63

G. Popa, A. Curtean-b?n?duc, D. B?n?duc, I. E. Florescu, A. Burcea et al.,

. Costache, Molecular markers reveal reduced genetic diversity in Romanian populations of 761 brown trout, Salmo trutta L., 1758 (Salmonidae), Acta Zoologica Bulgarica, vol.68, pp.399-406, 2016.

P. &. Presa and . Guyomard, Conservation of microsatellites in three species of salmonids, Journal, p.763, 1996.

, Fish Biology, vol.49, pp.1326-1329

P. Presa, F. Krieg, A. Estoup, and &. Guyomard, Diversité et gestion génétique de la truite commune: 765 apport de l'étude du polymorphisme des locus protéiques et microsatellites, Genetics Selection, vol.766, pp.183-202, 1994.

P. Presa, B. G. Pardo, P. Martinez, and &. Bernatchez, Phylogeographic congruence between mtDNA 768 and rDNA ITS markers in brown trout, Molecular Biology and Evolution, vol.19, issue.12, pp.2161-2175, 2002.

J. K. Pritchard, M. Stephens, and &. Donnelly, Inference of population structure using multilocus 770 genotype data, Genetics, vol.155, pp.945-959, 2000.

I. Rexroad, C. E. , R. L. Coleman, W. K. Hershberger, and &. Killefer, Thirty-eight polymorphic 772 microsatellite markers for mapping in rainbow trout, Journal of Animal Science, vol.80, pp.541-542, 2002.

W. R. Rice, Analyzing tables of statistical tests, Evolution, vol.43, pp.223-225, 1989.

L. Roule, Le peuplement des cours d'eau de la Corse en poissons, Bulletin Français de Pisciculture, vol.775, pp.61-62, 1933.

A. Sabatini, R. Cannas, M. C. Follesa, F. Palmas, A. Manunza et al., P. Serra & A

. Cau, Genetic characterization and artificial reproduction attempt of endemic Sardinian trout, 2011.

L. Salmo, 1758 (Osteichthyes, Salmonidae): Experiences in captivity, Italian Journal of 779 Zoology, vol.78, issue.1, pp.20-26

A. Sabatini, F. Orrù, R. Cannas, P. Serra, and &. Cau, Conservation and management of Salmo 781 (trutta) macrostigma in Sardinian freshwaters: first results of genetic characterization, Quaderni, vol.782, pp.335-340, 2006.

A. Sabatini, C. Podda, G. Frau, M. V. Cani, A. Musu et al., Restoration 784 of native Mediterranean trout Salmo cetti Rafinesque, 1810 (Actinopterygii, Salmonidae) 785 populations using an electric barrier as mitigation tool, The European Zoological Journal, 2018.

N. Sanz, Phylogeographic history of brown trout: a review, 2018.

, Brown trout: biology, ecology and management, pp.17-63

J. Schöffmann, S. Su?nik, and &. Snoj, Phylogenetic origin of Salmo trutta L 1758 from Sicily, based 790 on mitochondrial and nuclear DNA analyses, Hydrobiologia, vol.575, pp.51-55, 2007.

K. T. Scribner, J. R. Gust-&-r, and . Fields, Isolation and characterization of novel salmon 792 microsatellite loci: Cross-species amplification and population genetic applications, Canadian 793 Journal of Fisheries and Aquatic Sciences, vol.53, pp.833-841, 1996.

J. X. She, M. Autem, G. Kotoulas, N. Pasteur, and &. Bonhomme, Multivariate analysis of genetic 795 exchanges between Solea aegyptiaca and Solea senegalensis (Teleosts, Soleidae), Biological 796 Journal of the Linnean Society, vol.32, pp.357-371, 1987.

J. W. Sites and . Marshall, Empirical criteria for delimiting species, Annual Review of Ecology, p.798, 2004.

, Evolution, and Systematics, vol.35, pp.199-227

S. Baric, A. Riedl, A. Meraner, N. Medgyesy, R. Lackner et al., Alpine headwater 1025 streams as reservoirs of remnant populations of the Danubian clade of brown trout, Freshwater Biology, vol.55, p.866, 2010.

P. Berrebi, C. Tougard, S. Dubois, Z. Shao, I. Koutseri et al., Genetic diversity 1028 and conservation of the Prespa trout in the Balkans, International Journal of Molecular Sciences, vol.14, pp.23454-23470, 2013.

M. Cortey and J. L. García-marín, Evidence for phylogeographically informative sequence variation in the 1030 mitochondrial control region of Atlantic brown trout, Journal of Fish Biology, vol.60, pp.1058-1063, 2002.

M. Cortey, C. Pla, and J. L. García-marín, Historical biogeography of Mediterranean trout, Molecular 1032 Phylogenetics and Evolution, vol.33, pp.831-844, 2004.

M. Cortey, M. Vera, C. Pla, and J. L. Garcia-marin, Northern and Southern expansions of Atlantic brown 1034 trout (Salmo trutta) populations during the Pleistocene, Biological Journal of the Linnean Society, vol.97, pp.904-917, 2009.

N. Duftner, S. Weiss, N. Medgyesy, and C. Sturmbauer, Enhanced phylogeographic information about 1036 Austrian brown trout populations derived from complete mitochondrial control region sequences, Journal of Fish 1037 Biology, vol.62, pp.427-435, 2003.

M. Jadan, I. Strunjak-perovi?, N. Topi?-popovi?, and R. ?o?-rakovac, Three major phylogenetic lineages of 1039 brown trout (Salmo trutta Linnaeus, 1758) in the Krka River system (Croatia) revealed by complete mitochondrial 1040 DNA control region sequencing, Journal of Applied Ichthyology, vol.31, pp.192-196, 2015.

J. Kohout, A. ?edivá, A. Apostolou, T. Stefanov, S. Mari? et al., Genetic diversity 1042 and phylogenetic origin of brown trout Salmo trutta populations in eastern Balkans, Biologia, vol.68, pp.1229-1237, 2013.

S. Mari?, S. Su?nik-bajec, J. Schöffmann, V. Kostov, and A. Snoj, Phylogeography of stream-dwelling 1044 trout in the Republicof Macedonia and a molecular genetic basis for revision of the taxonomy proposed by S, 2017.

. Karaman, Hydrobiologia, vol.785, pp.249-260

A. Meraner, S. Baric, B. Pelster, and J. Dalla-via, Trout (Salmo trutta) mitochondrial DNA polymorphism in 1047 the centre of the marble trout distribution area, Hydrobiologia, vol.579, pp.337-349, 2007.

A. Meraner, P. Gratton, F. Baraldi, and A. Gandolfi, Nothing but a trace left? Autochthony and conservation 1049 status of Northern Adriatic Salmo trutta inferred from PCR multiplexing, mtDNA control region sequencing and 1050 microsatellite analysis, Hydrobiologia, vol.702, pp.201-213, 2013.

J. M. Pujolar, A. N. Lucarda, M. Simonato, and T. Patarnello, Restricted gene flow at the micro-and 1052 macro-geographical scale in marble trout based on mtDNA and microsatellite polymorphism, Frontiers in 1053 Zoology, vol.8, p.7, 2011.

A. Snoj, S. Mari?, S. Su?nik-bajec, P. Berrebi, S. Janjani et al., Phylogeographic structure 1055 and demographic patterns of brown trout in North-West Africa, Molecular Phylogenetics and Evolution, vol.61, pp.203-1056, 2011.

J. Suárez, J. M. Bautista, .. A. Almodóvar, and A. Machordom, Evolution of the mitochondrial control region 1058 in Paleartic brown trout (Salmo trutta) populations: the biogeographical role of the Iberian Peninsula, Heredity, vol.87, pp.1059-198, 2001.

S. Su?nik, A. Snoj, I. F. Wilson, D. Mrdak, and S. Weiss, Historical demography of brown trout (Salmo 1061 trutta) in the Adriatic drainage including the putative S. letnica endemic to Lake Ohrid, Molecular Phylogenetics 1062 and Evolution, vol.44, pp.63-76, 2007.

S. Zaccara, S. Trasforini, C. M. Antognazza, C. Puzzi, J. R. Britton et al., Morphological and 1064 genetic characterization of Sardinian trout Salmo cettii Rafinesque, 1810 and their conservation implications, 2015.

, Hydrobiologia, vol.760, pp.205-223

M. Vera, J. L. García-marín, P. Martinez, and C. Bouza, Phylogenetic diversity within the endemic brown 1067 trout Duero lineage: implications for conservation and management, Marine & Freshwater Research, vol.66, pp.1066-1068, 2015.

D. ?kraba, A. Be?iraj, I. ?ari?, I. I?anovi?, A. D?aferovi? et al.,

P. Simonovi?, Haplotype diversity of brown trout (Salmo trutta L.) populations from Una River drainage 1071 area in Bosnia and Herzegovina: Implications for conservation and fishery management, Acta Zoologica Bulgarica 1072, vol.69, pp.25-30, 2017.

M. Vera, I. Sourinejad, C. Bouza, R. Vilas, A. Pino-querido et al., , 2011.

, Phylogeography, genetic structure, and conservation of the endangered Caspian brown trout, Salmo trutta caspius 1075 (Kessler, 1877), from Iran, Hydrobiologia, vol.664, pp.51-67

S. Weiss, C. Schloötterer, H. Waidacher, and M. Jungwirth, Haplotype (mtDNA) diversity of brown trout, 2001.

, Salmo trutta in tributaries of the Austrian Danube: massive introgression of Atlantic basin fish by man or nature?, Molecular Ecology, vol.10, pp.1241-1246, 1078.

, Present study (*new haplotypes)

. Evanno, L(K) -posterior probability of K; stdev -standard deviation of L(K) from seven 1084 independent runs; ?K -an ad hoc quantity, predictor of the real number of clusters, Table S2 Hierarchical steps in estimating K (the number of genetic clusters) from STRUCTURE runs 1083 using the ?K method, 2005.

. K-l(k),

. Tassineta, . Maghjine, . Speloncellu, . Pozzi, A. Val-d'ese et al.,

U. Nd-step--roya, . Furcone, . Cantiano-hatchery, . Visso-hatchery, I. Ermolinus et al., Anapo & south step -Cantiano hatchery