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Φυλογεωγραφία Των Ενδημικών Ειδών Του Γένους Trachelipus (Isopoda

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Φυλογεωγραφία Των Ενδημικών Ειδών Του Γένους Trachelipus (Isopoda ΠΑΝΕΠΙΣΤΗΜΙΟ ΠΑΤΡΩΝ ΣΧΟΛΗ ΘΕΤΙΚΩΝ ΕΠΙΣΤΗΜΩΝ ΤΜΗΜΑ ΒΙΟΛΟΓΙΑΣ ΤΟΜΕΑΣ ΒΙΟΛΟΓΙΑΣ ΖΩΩΝ ΕΡΓΑΣΤΗΡΙΟ ΖΩΟΛΟΓΙΑΣ Φυλογεωγραφία των ενδημικών ειδών του γένους Trachelipus (Isopoda, Oniscidea) στην Ελλάδα ΠΡΟΓΡΑΜΜΑ ΜΕΤΑΠΤΥΧΙΑΚΩΝ ΣΠΟΥΔΩΝ “ΟΙΚΟΛΟΓΙΑ – ΔΙΑΧΕΙΡΙΣΗ ΚΑΙ ΠΡΟΣΤΑΣΙΑ ΦΥΣΙΚΟΥ ΠΕΡΙΒΑΛΛΟΝΤΟΣ” ΔΙΑΤΡΙΒΗ ΜΕΤΑΠΤΥΧΙΑΚΟΥ ΔΙΠΛΩΜΑΤΟΣ ΕΙΔΙΚΕΥΣΗΣ ΜΑΡΙΑ ΚΑΜΗΛΑΡΗ Βιολόγος Α.Μ. 401 ΠΑΤΡΑ, 2010 ΠΑΝΕΠΙΣΤΗΜΙΟ ΠΑΤΡΩΝ ΣΧΟΛΗ ΘΕΤΙΚΩΝ ΕΠΙΣΤΗΜΩΝ ΤΜΗΜΑ ΒΙΟΛΟΓΙΑΣ ΤΟΜΕΑΣ ΒΙΟΛΟΓΙΑΣ ΖΩΩΝ ΕΡΓΑΣΤΗΡΙΟ ΖΩΟΛΟΓΙΑΣ Φυλογεωγραφία των ενδημικών ειδών του γένους Trachelipus (Isopoda, Oniscidea) στην Ελλάδα ΠΡΟΓΡΑΜΜΑ ΜΕΤΑΠΤΥΧΙΑΚΩΝ ΣΠΟΥΔΩΝ “ΟΙΚΟΛΟΓΙΑ – ΔΙΑΧΕΙΡΙΣΗ ΚΑΙ ΠΡΟΣΤΑΣΙΑ ΦΥΣΙΚΟΥ ΠΕΡΙΒΑΛΛΟΝΤΟΣ” ΔΙΑΤΡΙΒΗ ΜΕΤΑΠΤΥΧΙΑΚΟΥ ΔΙΠΛΩΜΑΤΟΣ ΕΙΔΙΚΕΥΣΗΣ ΜΑΡΙΑ ΚΑΜΗΛΑΡΗ Βιολόγος Α.Μ. 401 ΠΑΤΡΑ, 2010 Μέλη της τριμελούς εξεταστικής επιτροπής Γιώργος Κίλιας, Αναπληρωτής Καθηγητής, Τομέας Γενετικής Βιολογίας Κυττάρου και ανάπτυξης Έλενα Κλώσσα – Κίλια, Επίκουρη Καθηγήτρια, Τομέας Βιολογίας Ζώων Σπύρος Σφενδουράκης, Επίκουρος Καθηγητής, Τομέας Βιολογίας Ζώων Επιβλέπουσα Καθηγήτρια Έλενα Κλώσσα – Κίλια Ευχαριστίες Η παρούσα Διατριβή αποτελεί την ερευνητική μου εργασία στο πλαίσιο του Μεταπτυχιακού Διπλώματος Ειδίκευσης του τμήματος Βιολογίας στην κατεύθυνση “Οικολογία – Διαχείριση και Προστασία Φυσικού Περιβάλλοντος”. Θα ήθελα να ευχαριστήσω θερμά τα μέλη της τριμελούς επιτροπής, κα Έλενα Κλώσσα-Κίλια, κ. Γιώργο Κίλια και κ. Σπύρο Σφενδουράκη για την εμπιστοσύνη που μου έδειξαν και την ελευθερία με την οποία μου επέτρεψαν να εργάζομαι στο εργαστήριο, να οργανώσω το πρόγραμμά μου και να φέρω εις πέρας το θέμα της διατριβής μου. Ήταν πάντα εκεί για να απαντήσουν τις όποιες απορίες ή να ακούσουν την «γκρίνια» μου για όποιες ατυχίες στα πειράματά μου. Ιδιαίτερο ευχαριστώ οφείλω στο Σπύρο Σφενδουράκη με τον οποίο συνεργάζομαι τα τελευταία 6 χρόνια. Οι εξορμήσεις μαζί του στο πεδίο είναι πάντα ένα πολύ καλύτερο και ποιοτικότερο μάθημα από αυτό μέσα στις άχρωμες αίθουσες του Πανεπιστημίου. Τον ευχαριστώ θερμά και για το ερευνητικό πρόγραμμα «Καραθεοδωρή» στο οποίο με συμπεριέλαβε ως κύρια ερευνήτρια και από το οποίο χρηματοδοτήθηκε ένα μέρος αυτής της διατριβής. Στο πλαίσιο της ερευνητικής μου εργασίας είχα την τύχη να εργάζομαι τόσο στον ερευνητικό χώρο του κ. Σφενδουράκη στο εργαστήριο Ζωολογίας, όσο και στον ερευνητικό χώρο του κ. Κίλια στο εργαστήριο Γενετικής. Ως εκ τούτου είχα την ευκαιρία να συνεργαστώ με πολλούς ανθρώπους διαφορετικών αντικειμένων, να μάθω πολλά από αυτούς και να περάσουν πολύ ευχάριστα τα τρία αυτά χρόνια. Ελπίζοντας λοιπόν να μην ξεχνώ κανέναν, ευχαριστώ για το ευχάριστο κλίμα, τα αμέτρητα γέλια, τα ομαδικά ξενύχτια στο εργαστήριο και όλες τις στιγμές που περάσαμε μαζί τη Χριστίνα Κασσάρα, την Εβίτα Πίττα, Ονούφριο Μεττούρη, το Μιχάλη Ροβάτσο και τη Σπυριδούλα Κράιτσεκ. Ξεχωριστά οφείλω να ευχαριστήσω το Στέφανο Μαρτιμιανάκη για την καθοδήγησή του στα πρώτα μου πειράματα στο πάγκο και την εκμάθηση των εργαστηριακών τεχνικών. Για μένα ο εργαστηριακός πάγκος της γενετικής ήταν κάτι καινούριο και στην αρχή ομολογώ «αγχωτικό». Ωστόσο ήταν πάντα με πολλή υπομονή δίπλα μου δίνοντας περισσότερο βάση στο επιστημονικό «γιατί» παρά στο τεχνικό «πρέπει» της όποιας πειραματικής διαδικασίας. Επίσης θα ήθελα να ευχαριστήσω θερμά το Δρ. Γιώργο Τρυφωνόπουλο για τη μεγάλη του βοήθεια στην εκμάθηση και κατανόηση των υπολογιστικών προγραμμάτων που χρησιμοποίησα στην παρούσα μελέτη. Μιας άχαρης διαδικασίας για πολλούς αλλά απολύτως απαραίτητης για όλους. Με τη Χαρά Παπαϊωάννου μοιραστήκαμε τις ίδιες καρέκλες, τις ίδιες πιπέτες και τις ίδιες «επιστημονικές ανησυχίες» στο εργαστήριο της Γενετικής. Ταιριάξαμε στον τρόπο δουλειάς και συνεννόησης αλλά ευτυχώς και στην «ευχάριστη διάθεση» που μας διακρίνει. Χαίρομαι πολύ που θα συνεχίσουμε να δουλεύουμε μαζί. Δε θα μπορούσα να παραλείψω τους γονείς μου Θανάση και Ευαγγελία, την αδερφή μου Ελένη και φυσικά τη γιαγιά μου Μαίρη που τόσα χρόνια με στηρίζουν ηθικά, ψυχολογικά και οικονομικά. Ξέρω πως κάνουν τα θέλω μου θέλω τους ακόμα και όταν δεν το πολυθέλουν… Τέλος θέλω να ευχαριστήσω το Δημήτρη μου που με βοήθησε τόσο στις δειγματοληψίες όσο και στη συγγραφή της διατριβής μου με εύστοχες διορθώσεις και προτάσεις. Ο καλός του λόγος και η ανοιχτή του αγκαλιά ήταν το αγχολυτικό μου…. Στην γιαγιά μου Μαίρη, Την πιο φανατική μου θαυμάστρια… ΠΕΡΙΕΧΟΜΕΝΑ ΠΕΡΙΛΗΨΗ-------------------------------------------------------- 5 ABSTRACT -------------------------------------------------------- 8 A. ΕΙΣΑΓΩΓΗ ---------------------------------------------------- 11 1. ΓΕΝΙΚΑ ΣΤΟΙΧΕΙΑ ΓΙΑ ΤΗΝ ΤΑΞΗ ΤΩΝ ΙΣΟΠΟΔΩΝ ----------------- 11 1.1. ΙΣΤΟΡΙΚΑ ΣΤΟΙΧΕΙΑ ΚΑΙ ΣΤΟΙΧΕΙΑ ΕΞΕΛΙΞΗΣ ------------------------------------------ 11 1.2. ΤΑ ΧΕΡΣΑΙΑ ΙΣΟΠΟΔΑ -------------------------------------------------------------------12 1.2.1. Εξωτερική μορφολογία -----------------------------------------------------------------13 2. ΓΕΝΙΚΑ ΠΕΡΙ ΟΙΚΟΛΟΓΙΑΣ ΚΑΙ ΒΙΟΛΟΓΙΑΣ ΤΟΥ ΓΕΝΟΥΣ TRACHELIPUS BUDDE- LUND, 1908------------------------------------------------------- 15 2.1. ΟΙΚΟΛΟΓΙΑ -------------------------------------------------------------------------------15 2.2. ΑΝΑΠΑΡΑΓΩΓΗ – ΑΝΑΠΤΥΞΗ ------------------------------------------------------------16 3.ΤΑΞΙΝΟΜΗΣΗ - ΓΕΩΓΡΑΦΙΚΗ ΚΑΤΑΝΟΜΗ--------------------------- 18 3.1. ΔΙΑΓΝΩΣΤΙΚΟΙ ΧΑΡΑΚΤΗΡΕΣ ΤΟΥ ΓΕΝΟΥΣ ----------------------------------------------21 4. ΠΑΛΑΙΟΓΕΩΓΡΑΦΙΚΑ ΣΤΟΙΧΕΙΑ ΤΟΥ ΕΛΛΑΔΙΚΟΥ ΧΩΡΟΥ ------------- 22 5. ΦΥΛΟΓΕΩΓΡΑΦΙΑ ----------------------------------------------- 31 5.1. ΕΡΓΑΛΕIΑ ΣΤΗΝ ΥΠΗΡΕΣΙΑ ΤΗΣ ΦΥΛΟΓΕΩΓΡΑΦΙΑΣ------------------------------------- 34 5.1.1. Μοριακοί χαρακτήρες «εναντίον» μορφολογικών ------------------------------------- 36 5.2. ΧΡΗΣΗ ΤΟΥ MTDNA ΣΤΗ ΜΕΛΕΤΗ ΤΩΝ ΠΛΗΘΥΣΜΩΝ --------------------------------- 37 5.2.1. Προέλευση του mt DNA -------------------------------------------------------------- 37 5.2.2. Ιδιότητες του mtDNA---------------------------------------------------------------- 38 6. ΕΡΕΥΝΗΤΙΚΟ ΠΡΟΒΛΗΜΑ ---------------------------------------- 42 Β. ΜΕΘΟΔΟΛΟΓΙΑ ΚΑΙ ΥΛΙΚΑ -------------------------------------- 45 1. ΣΥΛΛΟΓΗ ΔΕΙΓΜΑΤΩΝ ------------------------------------------ 45 1 2. ΤΑ ΜΙΤΟΧΟΝΔΡΙΑΚΑ ΓΟΝΙΔΙΑ ΤΗΣ ΜΕΛΕΤΗΣ ---------------------- 51 3. ΕΡΓΑΣΤΗΡΙΑΚΕΣ ΑΝΑΛΥΣΕΙΣ ------------------------------------- 52 3.1. ΠΕΙΡΑΜΑΤΙΚΗ ΠΟΡΕΙΑ ------------------------------------------------------------------ 52 3.1.1. Εξαγωγή Ολικού Γενωμικού DNA ---------------------------------------------------- 52 3.1.2. Ηλεκτροφόρηση Ολικού Γενωμικού DNA--------------------------------------------- 53 3.1.3. Πολλαπλασιασμός συγκεκριμένων τμημάτων DNA με τη μέθοδο της αλυσιδωτής αντίδρασης πολυμεράσης (PCR) ------------------------------------------------------------- 54 3.1.4. Καθαρισμός του πολλαπλασιασμένου τμήματος των γονιδίων COI και 16S rRNA--- 57 3.1.5. Καθορισμός της αλληλουχίας νουκλεοτιδίων των επιλεγμένων τμημάτων των μιτοχονδριακών γονιδίων-------------------------------------------------------------------- 58 4. ΣΤΑΤΙΣΤΙΚΗ ΕΠΕΞΕΡΓΑΣΙΑ ΤΩΝ ΔΕΔΟΜΕΝΩΝ THΣ ΑΝΑΛΥΣΗΣ ΑΛΛΗΛΟΥΧΙΑΣ --------------------------------------------------- 60 4.1. ΣΤΟΙΧΙΣΗ ΑΛΛΗΛΟΥΧΙΩΝ -------------------------------------------------------------- 60 4.2. ΕΛΕΓΧΟΣ ΔΕΔΟΜΕΝΩΝ ΓΙΑ ΟΜΟΠΛΑΣΙΑ ΚΑΙ ΚΟΡΕΣΜΟ-------------------------------- 62 4.3. ΕΠΕΞΕΡΓΑΣΙΑ ΤΩΝ ΣΤΟΙΧΙΣΜΕΝΩΝ ΑΛΛΗΛΟΥΧΙΩΝ----------------------------------- 64 4.3.1. Εκτίμηση γενετικών αποστάσεων ----------------------------------------------------- 65 4.3.2. Επιλογή του καταλληλότερου μοντέλου νουκλεοτιδικής υποκατάστασης ------------ 66 4.4. ΑΝΑΛΥΣΗ ΦΑΙΝΕΤΙΚΩΝ ΚΑΙ ΦΥΛΟΓΕΝΕΤΙΚΩΝ ΣΧΕΣΕΩΝ-------------------------------- 67 4.4.1. Μέθοδος Σύνδεσης Γειτόνων (Neighbor-Joining)----------------------------------- 68 4.4.2. Η μέθοδος της μέγιστης φειδωλότητας (Maximum Parsimony) --------------------- 69 4.4.3. Μπεϊεσιανή συμπερασματολογία ------------------------------------------------------ 70 4.5. ΑΝΕΞΑΡΤΗΤΗ Η ΣΥΝΔΥΑΣΜΕΝΗ ΑΝΑΛΥΣΗ ---------------------------------------------- 73 4.6. ΑΝΑΛΥΣΗ ΜΟΡΙΑΚΗΣ ΔΙΑΚΥΜΑΝΣΗΣ – ANALYSIS OF MOLECULAR VARIANCE (AMOVA) ----------------------------------------------------------------------------------------------- 76 Γ. ΑΠΟΤΕΛΕΣΜΑΤΑ ----------------------------------------------- 77 1. ΑΝΑΛΥΣΗ ΑΛΛΗΛΟΥΧΙΑΣ ΜΙΤΟΧΟΝΔΡΙΑΚΩΝ ΓΟΝΙΔΙΩΝ------------- 77 1.1. ΑΝΑΛΥΣΗ ΤΟΥ ΓΕΝΕΤΙΚΟΥ ΤΟΠΟΥ 16S RRNA------------------------------------------- 77 1.1.1. Νουκλεοτιδική σύσταση και Γενετική ποικιλότητα των μελετηθέντων πληθυσμών--- 77 1.1.2. Έλεγχος Ομοπλασίας------------------------------------------------------------------ 84 2 1.1.3. Εκτίμηση γενετικών αποστάσεων ----------------------------------------------------- 85 1.1.4. Φαινετικές και φυλογενετικές σχέσεις των μελετηθέντων πληθυσμών -------------- 88 1.1.5. Ανάλυση Μοριακής Διακύμανσης (AMOVA) – Δίκτυο Ελαχίστων Αποστάσεων (MSN) ----------------------------------------------------------------------------------------------- 93 1.1.5.1. Ομαδοποίηση βάσει γεωγραφικής προέλευσης -------------------------------------- 93 1.1.5.2. Ομαδοποίηση βάσει φυλογενετικής συγγένειας ------------------------------------- 97 1.2. ΑΝΑΛΥΣΗ ΤΟΥ ΓΕΝΕΤΙΚΟΥ ΤΟΠΟΥ COI ------------------------------------------------- 99 1.2.1. Νουκλεοτιδική σύσταση και γενετική ποικιλότητα των μελετηθέντων πληθυσμών -- 99 1.2.2. Έλεγχος Ομοπλασίας ---------------------------------------------------------------- 104 1.2.3. Εκτίμηση γενετικών αποστάσεων ---------------------------------------------------- 105 1.2.4. Φαινετικές και φυλογενετικές σχέσεις των μελετηθέντων πληθυσμών ------------- 108 1.2.5. Ανάλυση Μοριακής Διακύμανσης (AMOVA)------------------------------------------113
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