| Sažetak | Organisation and diversity of the eukaryotic cells are well documented phenomena today, so it is already known
scientific theory that LECA (the Last Eukaryotic Common Ancestor) harboured mitochondrion, nucleus,
endoplasmic reticulum made of bacterial lipids, sex, meiosis, and eukaryotic life cycle. None of the
aforementioned traits has been found in prokaryotes. The origin of those eukaryotes traits has, on the other side,
been an unresolved issue for many years. It is questionable whether the mitochondrion (bacterial endosymbiont)
entered the archaeal host cell prior to the formation of the nucleus or later; it has never been systematically studied
if LECA had a single or many nuclei; it has not been quantified how many gene duplications there were in LECA,
and what is their origin. Furthermore, cladistic terminology is often misapplied in molecular evolution and studies
are rarely based on taxon-rich sampling, meaning that eukaryotic diversity is not well covered. This dissertation,
hence, aims to discuss cladistics and its interpretation in theory, with emphasis on the definition of eukaryotes;
and practically, by analyses, to shed some light on the genome organization, morphology, and physiology of
LECA. Eukaryotes/Eukarya are defined as a monophyletic, holophyletic group with polyphyletic, reticulated
origin. Because of the reticulated origin of eukaryotes and because mitochondria and the nucleus are not regarded
as prokaryotes anymore, both Bacteria and Archaea are paraphyletic, i.e., monophyletic groups. Many
duplications were present in LECA and the Bacteria-derived ones were found to be prevalent what suggests that
mitochondria-early hypothesis might be correct. Except for the genes that originated from plastid acquisition
(Cyanobacteria), no specific genes were found within eukaryotic supergroups, suggesting that differential loss
and genome duplications are the major forces of the eukaryotic evolution. Ubiquity of the multinucleate state
across the eukaryotic domain is presented. Traits annotated on the eukaryotic tree were multinucleate state
presence and absence, open vs. closed nuclear division, as well as 'control traits' for which it is known to be
ancestral to LECA (presence of sex, mitochondria) or for which it is known not to be ancestral to LECA (plastid,
polyploidy). Ancestral state reconstruction did not reject the hypothesis that LECA was multinucleated, similar to
modern aseptate fungi or myxomycetes, and exhibited closed nuclear division. It is confirmed (i.e., not rejected)
that LECA was sexual, had mitochondria, did not have plastid and was not polyploid. The results of ancestral state
investigations presented in this work indicate that, contrary to popular beliefs, LECA was likely not a uninucleate
cell, from which it follows that uninuclear eukaryotes possibly represent highly specialized forms, of which some,
such as Excavata might even have originated long time ago from LECA's gametes. |
| Sažetak (hrvatski) | Raznolikost eukariota i organizacija njihovih stanica danas su već dobro poznati pa se može smatrati znanstvenom
teorijom da je LECA (engl. Last Eukaryotic Common Ancestor, Posljednji zajednički predak eukariota) imao je
mitohondrij, jezgru, unutarstaničnu mrežu membrana građenu od bakterijskih lipida, spol, mejozu i eukariotski
životni ciklus. U prokariota, usporedbe radi, ne postoji ni jedno od ovih obilježja. Usprkos dobrom poznavanju
njihove građe, postanak eukariota i dalje je jedan od neriješenih problema moderne znanosti. Ne zna se je li
mitohondrij (bakterijski endosimbiont) ušao u arheju prije ili nakon formacije jezgre; nikad nije utvrđeno je li
LECA imao samo jednu ili je imao više jezgara; do sada nije određeno koliko je LECA imao dupliciranih gena i
koje im je porijeklo. Uza sve to, u molekularnoj evoluciji često se pogrešno koristi terminologija sistematike, a
radovi najčešće ne uključuju veliku raznolikost, tj. nije pokriveno mnogo svojti. Ciljevi ove disertacije jesu
teoretski raspraviti terminologiju sistematike i njezinu interpretaciju, s naglaskom na definiciju eukariota; kao i
istražiti organizaciju genoma, morfologiju i fiziologiju LECA-e praktičnim analizama. Eukarioti
(Eukaryota/Eukarya) su definirani kao monofiletska; holofiletska skupina polifiletskog postanka. Zbog hibridnog
postanka eukariota i budući da se mitohondrij i jezgra više ne smatraju prokariotima, i bakterije (Bacteria) i arheje
(Archaea) su parafiletske tj. monofiletske skupine. Otkriveno je da je LECA imala mnogo duplikacija i da je
najviše onih koje potječu od bakterija što ide u prilog hipotezi da je mitohondrij bio prisutan tijekom same
eukariogeneze. Osim plastidnih gena koji su porijeklom iz cijanobakterija (Cyanobacteria), nisu pronađeni
jedinstveni geni niti u jednoj supergrupi što znači da su veliki gubitci dijelova genoma i duplikacije gena glavne
sile evolucije eukariotskog genoma. Višejezgrene stanice su učestale među eukariotima i u disertaciji je prikazana
njihova raznolikost. Na stablu eukariota označene su prisutnost i odsutnost višejezgrenih stanica te otvorena i
zatvorena dioba jezgre, kao i „kontrolna svojstva“, tj. ona za koja se zna da li su predačka LECA-i (spol,
mitohondrij) i ona za koja se zna da nisu (plastid, poliploidija). Rekonstrukcija predačkih svojstava nije odbacila
pretpostavke da je LECA bila višejezgrena, vjerojatno slična današnjim aseptičnim gljivama i sluznjačama
(Myxomycetes), kao ni da je imala zatvorenu diobu jezgri. Potvrđeno je također, tj. nije odbačeno, da je LECA
bila spolni organizam, da je imala mitohondrije, da nije imala plastide i da nije bila poliploidna. Suprotno
uvriježenom mišljenju, LECA najvjerojatnije nije bila jednojezgreni organizam i prema tome jednojezgreni
jednostanični eukarioti vjerojatno predstavljaju visokospecijalizirane organizme, od kojih neki poput supergrupe
Excavata—smisleno nagađanje—možda čak potječu od LECA-inih gameta. |
