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UNIVERZA V LJUBLJANI BIOTEHNIŠKA FAKULTETA Gašper PUSTOVRH MOLEKULARNA FILOGENIJA IN POPULACIJSKO GENETSKA STRUKTURA MARMORIRANE POSTRVI (Salmo marmoratus) V SLOVENIJI DOKTORSKA DISERTACIJA Ljubljana, 2013 UNIVERZA V LJUBLJANI BIOTEHNIŠKA FAKULTETA Gašper PUSTOVRH MOLEKULARNA FILOGENIJA IN POPULACIJSKO GENETSKA STRUKTURA MARMORIRANE POSTRVI (Salmo marmoratus) V SLOVENIJI DOKTORSKA DISERTACIJA MOLECULAR PHYLOGENY AND POPULATION GENETIC STRUCTURE OF MARBLE TROUT (Salmo marmoratus) IN SLOVENIA DOCTORAL DISSERTATION Ljubljana, 2013 Pustovrh G. Molekularna filogenija in populacijsko genetska struktura marmorirane postrvi v Sloveniji. Dokt. disertacija. Ljubljana, Univ. v Ljubljani, Biotehniška fakulteta, 2013 Na podlagi Statuta Univerze v Ljubljani ter po sklepu Senata Biotehniške fakultete in Senata Univerze z dne 27. september 2010, je bilo potrjeno, da kandidat izpolnjuje pogoje za neposreden prehod na doktorski študij bioloških in biotehniških znanosti ter opravljanje doktorata iz področja genetike. Za mentorico je bila imenovana doc. dr. Simona Sušnik Bajec in somentorja dr. Aleš Snoj viš. znan. sod. Komisija za oceno in zagovor: Predsednik: doc. dr. Jernej JAKŠE Univerza v Ljubljani, Biotehniška fakulteta, Oddelek za agronomijo Član: doc. dr. Simona SUŠNIK BAJEC Univerza v Ljubljani, Biotehniška fakulteta, Oddelek za zootehniko Član: dr. Aleš SNOJ, viš. znan. sod. Univerza v Ljubljani, Biotehniška fakulteta, Oddelek za zootehniko Član: doc. dr. Elena VARLJEN BUŽAN Univerza na Primorskem, Fakulteta za matematiko, naravoslovje in informacijske tehnologije, Oddelek za biodiverziteto Datum zagovora: 16.05.2013 Naloga je rezultat lastnega raziskovalnega dela. Gašper Pustovrh II Pustovrh G. Molekularna filogenija in populacijsko genetska struktura marmorirane postrvi v Sloveniji. Dokt. disertacija. Ljubljana, Univ. v Ljubljani, Biotehniška fakulteta, 2013 KLJUČNA DOKUMENTACIJSKA INFORMACIJA ŠD Dd DK UDK 597.2/.5:575.8(043.3)=163.6 KG filogenija/filogeografija/populacijska genetika/ribe/rod Salmo/marmorirana postrv/Salmo marmoratus KK AGRIS L10/8100 AV PUSTOVRH, Gašper, dr. vet. med. SA SUŠNIK BAJEC, Simona (mentorica) / SNOJ, Aleš (somentor) KZ Sl-1230 Domžale, Groblje3 ZA Univerza v Ljubljani, Biotehniška fakulteta, Podiplomski študij bioloških in biotehniških znanosti, področje genetike LI 2013 IN MOLEKULARNA FILOGENIJA IN POPULACIJSKO GENETSKA STRUKTURA MARMORIRANE POSTRVI (Salmo marmoratus) V SLOVENIJI TD Doktorska disertacija OP XIV, 106, 8 pregl., 27 sl., 4 pril., 197 vir. IJ sl JI sl/en AI Osnovni namen opravljene raziskave je bil podati evolucijsko zgodovino ter razrešiti populacijsko genetske odnose marmorirane postrvi v Sloveniji. Raziskavo smo razdelili v dva sklopa. (i) V prvem sklopu smo skušali določiti filogenetske odnose znotraj rodu Salmo, pri čemer se zaradi celostnega pogleda nismo osredotočili zgolj na marmorirano postrv, ampak tudi na ostale vrste, linije oz. populacije rodu. S statističnimi programi MrBayes, Garli in BEAST smo na osnovi 22 nukleotidnih zaporedij nepovezanih lokusov ugotovili, da je rod Salmo sestavljen iz petih vrst: atlantski losos (Salmo salar), belvica (Salmo ohridanus), potočna postrv (Salmo trutta), marmorirana postrv (Salmo marmoratus) in mehkoustna postrv (Salmo obtusirostris). Pri tem je marmorirana postrv najbolj sorodna potočni postrvi in je sestavljena iz dveh skupin, ki predstavljata južne in severne populacije. (ii) V drugem sklopu smo proučevali populacijsko genetsko strukturo marmorirane postrvi. V Sloveniji je znanih osem genetsko čistih populacij marmorirane postrvi, ter številne populacije, ki so sestavljene iz različnega deleža marmorirane ter potočne postrvi (cona križanja). S postavitvijo genotipizacijskega sistema 36 SNP označevalcev, ki ločujejo marmorirano od potočne postrvi AT in DA filogenetske linije, smo pri analizi cone križanja ugotovili, da je delež genoma marmorirane postrvi in genetsko čistih marmoriranih postrvi tu relativno visok, pri nekaterih populacijah pa marmorirane postrvi v populaciji celo prevladujejo. Ker je osem genetsko čistih populacij popolnoma izoliranih ter se tako genetsko kot tudi fenotipsko med seboj razlikujejo, smo v jedrnem genomu poiskali SNP-je, ki so zanje variabilni in omenjene populacije analizirali. Ugotovili smo, da so si fenotipsko podobne populacije idrijskega na eni strani in soškega porečja na drugi strani, tudi genetsko sorodne. Da bi lahko pojasnili razlike v fenotipu, smo preverili hipotezo o možnem prehodu potočne postrvi iz sosednjega donavskega v jadransko porečje. Pri analizi populacij križanja v vzhodnem delu idrijskega porečja smo ugotovili povečano prisotnost donavske filogenetske linije, kar bi lahko potrdilo postavljeno hipotezo in pojasnilo značilen idrijski fenotip. III Pustovrh G. Molekularna filogenija in populacijsko genetska struktura marmorirane postrvi v Sloveniji. Dokt. disertacija. Ljubljana, Univ. v Ljubljani, Biotehniška fakulteta, 2013 KEY WORDS DOCUMENTATION DN Dd DC UDC 597.2/.5:575.8(043.3)=163.6 CX phylogeny/filogeography/population genetics/fish/genus Salmo/marble trout/Salmo marmoratus CC AGRIS L10/8100 AU PUSTOVRH, Gašper AA SUŠNIK BAJEC, Simona (supervisor) / SNOJ, Aleš (supervisor) PP SI-1230 Domžale, Groblje3 PB University of Ljubljana, Biotechnical faculty, Postgraduate Study of Biological and Biotechnical Science, Field: Genetics PY 2013 TI MOLECULAR PHYLOGENY AND POPULATION GENETIC STRUCTURE OF MARBLE TROUT (Salmo marmoratus) IN SLOVENIA DT Doctoral Dissertation NO XIV, 106 p., 8 tab., 27 fig., 4 ann., 197 ref. LA sl AL sl/en AB The main purpose of the research was to resolve evolutionary history and population genetic structure of marble trout in Slovenia. The research was carried out in two parts. (i) In the first part we tried to determine the phylogenetic relationships within the Salmo genus, concentrating not only on the marble trout, but also on other species, lineages and populations in the genus. Based on 22 sequences of uncorrelated loci and using statistical programs such as MrBayes, Garli and BEAST we concluded that the genus Salmo consists of five species: atlantic salmon (Salmo salar), ohrid trout (Salmo ohridanus), brown trout (Salmo trutta), marble trout (Salmo marmoratus) and softmouth trout (Salmo obtusirostris). In the genus, marble trout is closely related to brown trout and is composed of two groups, representing the northern and southern populations. (ii) In the second part we tried to determine the genetic structure of marble trout populations. In Slovenia, there are eight genetically pure populations of marble trout and several populations that are composed of different percentage of marble and brown trout genes (hybridization zone). Using genotyping system based on 36 SNP markers that can separate marble from brown trout of AT and DA phylogenetic lineage, we tested populations found in hybridization zone. We estimated that the proportion of marble trout genome and number of genetically pure marble trout in the hybridization zone is relatively high and that marble trout in some populations is dominating. Obviously, eight genetically pure populations are not communicating and are genetically and phenotypically different. We compared different parts of nuclear genome and found five SNPs that we used to test the eight populations. We found that phenotypically connected populations of Idrijca river basin on one hand and the Soča river basin on the other hand, are also genetically related. In order to explain the differences in phenotype, we tested the hypothesis of a possible ancient migration of brown trout from the neighboring Danube to the Adriatic basin. In the analysis of hybrid populations of the eastern part of the Idrija basin, we found an increased presence of the DA phylogenetic lineage, which tends to prove the hypothesis and explains Idrijca basin characteristic marble trout phenotype. IV Pustovrh G. Molekularna filogenija in populacijsko genetska struktura marmorirane postrvi v Sloveniji. Dokt. disertacija. Ljubljana, Univ. v Ljubljani, Biotehniška fakulteta, 2013 KAZALO VSEBINE str. Ključna dokumentacijska informacija (KDI) ....................................................................... III Key words documentation (KDW) ..................................................................................... IV Kazalo preglednic ................................................................................................................ IX Kazalo slik ............................................................................................................................. X Kazalo prilog ..................................................................................................................... XIII Okrajšave in simboli ..........................................................................................................XIV 1 UVOD ............................................................................................................................ 1 1.1 NAMEN DELA .......................................................................................................... 1 1.2 HIPOTEZE ................................................................................................................. 3 2 PREGLED OBJAV ...................................................................................................... 5 2.1 MARMORIRANA POSTRV ..................................................................................... 5 2.1.1 Telesne značilnosti ...........................................................................................
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  • Anadromy, Potamodromy and Residency in Brown Trout Salmo Trutta: the Role of Genes and the Environment

    Anadromy, Potamodromy and Residency in Brown Trout Salmo Trutta: the Role of Genes and the Environment

    Anadromy, potamodromy and residency in brown trout Salmo trutta: the role of genes and the environment Ferguson, A., Reed, T. E., Cross, T. F., McGinnity, P., & Prodohl, P. A. (2019). Anadromy, potamodromy and residency in brown trout Salmo trutta: the role of genes and the environment. Journal of Fish Biology. https://doi.org/10.1111/jfb.14005 Published in: Journal of Fish Biology Document Version: Publisher's PDF, also known as Version of record Queen's University Belfast - Research Portal: Link to publication record in Queen's University Belfast Research Portal Publisher rights Copyright 2019 the authors. This is an open access article published under a Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited. General rights Copyright for the publications made accessible via the Queen's University Belfast Research Portal is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The Research Portal is Queen's institutional repository that provides access to Queen's research output. Every effort has been made to ensure that content in the Research Portal does not infringe any person's rights, or applicable UK laws. If you discover content in the Research Portal that you believe breaches copyright or violates any law, please contact [email protected]. Download date:30. Sep. 2021 Received: 13 March 2019 Accepted: 9 May 2019 DOI: 10.1111/jfb.14005 REVIEW PAPER FISH Anadromy, potamodromy and residency in brown trout Salmo trutta: the role of genes and the environment Andrew Ferguson1 | Thomas E.
  • Evolucijska Istorija Kompleksa Potočne Pastrmke Salmo Trutta L

    Evolucijska Istorija Kompleksa Potočne Pastrmke Salmo Trutta L

    Univerzitet u Beogradu Biološki fakultet mr Saša P. Marić Evolucijska istorija kompleksa potočne pastrmke Salmo trutta L. 1758 na području Republike Srbije i značaj za ribarstvo Doktorska disertacija Beograd, 2005. Univerzitet u Beogradu Biološki fakultet mr Saša P. Marić Evolucijska istorija kompleksa potočne pastrmke Salmo trutta L. 1758 na području Republike Srbije i značaj za ribarstvo Mentor: dr Predrag Simonović – vanredni profesor Biološki fakultet Univerzitet u Beogradu Članovi komisije: dr Jelka Crnobrnja - Isailović – naučni saradnik Institut za biološka istraživanja «Siniša Stanković» Beograd dr Aleš Snoj – naučni saradnik Biotehnički fakultet Univerzitet u Ljubljani Datum odbrane: Doktorska disertacija Beograd, 2005. III Zahvalnica Zahvalnica Zahvaljujem se svima koji su mi na bilo koji način olakšali rad na izradi disertacije i koji su svojim zalaganjem i nesebičnošću doprineli da ona ugleda svetlost dana. Srdačno se zahvaljujem mentoru i članovima Komisije na korektnom i profesionalnom odnosu punom razumevanja. Zahvaljujem se mentoru Prof. dr Predragu Simonoviću, koji mi je, osim istina iz ove nauke, pokazao da se autoritet i poštovanje stiču jedino znanjem i korektnim odnosom prema kandidatu. Posebno se zahvaljujem za ukazano poverenje i neograničenu slobodu. Zahvaljujem se dr Alešu Snoju koji je rukovodio laboratorijskim radom i koji me je upoznao sa metodama molekularne genetike. Posebno mu se zahvaljujem na posvećenom vremenu, izuzetnom stpljenju, ukazanom poverenju, ustupljenoj literaturi, savetima, kao i odnosu za koji sigurno mogu reći da prevazilazi granice profesionalnog. Takođe se zahvaljujem dr Jelki Crnobrnji – Isailović koja mi je izašla u susret kada je to bilo neophodno, i u najkraćem roku pregledala disertaciju dajući veoma korisne sugestije. Zahvaljujem se Nenadu Sekuliću iz Zavoda za zaštitu prirode Srbije na ustupljenom materijalu sa područja Kosova i Metohije, kao i kolegama Prof.