Genomic phylostratigraphy

Abstract

Makroevolucija, često definirana kao “evolucija iznad razine vrste”, tradicionalno se proučava analizom fosila, komparativnom morfologijom ili tzv. evo-devo pristupom. Korištenjem komparativne genomike moguće je rekonstruirati evolucijsku povijest na dodatnoj razini, metodom genomske filostratigrafije. Genomsku filostratigrafiju razvio je Tomislav Domazet-Lošo s Instituta Ruđer Bošković u Zagrebu. Ova novija statistička metoda koristi se za povezivanje evolucijskog porijekla obitelji osnivačkih gena s određenim makroevolucijskim tranzicijama. Pretpostavka je da će porijeklo složenih fenotipskih inovacija biti udruženo s pojavom takvih osnivačkih gena čiji se potomci mogu pronaći u danas živućim organizmima. Suština metode je podjela genoma u tzv. filostratume – skupine gena definiranih na temelju njihovog evolucijskog porijekla. Ovom je metodom postalo moguće identificirati sve orphan gene koji su doveli do postojećih genoma unutar evolucijskih linija, ali i pratiti važne makroevolucijske adaptacije kao što su pojava zametnih listića ili porijeklo gena povezanih uz nastanak raka. Također, genomska filostratigrafija potvrdila je postojanje filotipske faze u razvoju životinja i biljaka. Ipak, mogu li računalne simulacije stvarno obuhvatiti pravu kompleksnost evolucije?Macroevolution, which is often defined as “evolution above the species level”, is traditionally studied by fossil analysis, comparative morphology or evo-devo approaches. With the use of comparative genomics one can nowadays reconstruct the evolutionary history on additional level of analysis by genomic phylostratigraphy. Genomic phylostratigraphy was developed by Tomislav Domazet-Lošo at the Ruđer Bošković Institute in Zagreb, Croatia. This novel statistical method is used to correlate the evolutionary origin of founder gene families to particular macroevolutionary transitions. It is assumed that the origin of complex phenotypic innovations will be accompanied by the emergence of such founder genes, the descendants of which can still be traced in extant organisms. Method is based on the genome divison into phylostrata - classes of genes according to their evolutionary origin in the history of life. With this method it has become possible to identify all orphan genes within the evolutionary lineages that have led to a particular extant genome and to trace the origin of major macroevolutionary adaptations such as emergence of germ layers or origin of cancer genes. Also, genomic phylostratigraphy confirmed the existence of phylotypic stage in animal and plant development. However, how well can computer simulations really capture the true complexity of evolution