Macroevolutionary dynamics of gene family gain and loss along multicellular eukaryotic lineages

Domazet-Lošo, Mirjana; Široki, Tin; Šimičević, Korina; Domazet-Lošo, Tomislav (2024) Macroevolutionary dynamics of gene family gain and loss along multicellular eukaryotic lineages. Nature Communications, 15 (1). ISSN 2041-1723

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Abstract

The gain and loss of genes fluctuate over evolutionary time in major eukaryotic clades. However, the full profile of these macroevolutionary trajectories is still missing. To give a more inclusive view on the changes in genome complexity across the tree of life, here we recovered the evolutionary dynamics of gene family gain and loss ranging from the ancestor of cellular organisms to 352 eukaryotic species. We show that in all considered lineages the gene family content follows a common evolutionary pattern, where the number of gene families reaches the highest value at a major evolutionary and ecological transition, and then gradually decreases towards extant organisms. This sup- ports theoretical predictions and suggests that the genome complexity is often decoupled from commonly perceived organismal complexity. We con- clude that simplification by gene family loss is a dominant force in Phanerozoic genomes of various lineages, probably underpinned by intense ecological specializations and functional outsourcing.

Item Type:	Article
Uncontrolled Keywords:	gene family gain and loss; multicellular eukaryotic lineages; organismal complexity; ecological specializations; functional outsourcing
Subjects:	NATURAL SCIENCES > Biology > Genetics, Evolution and Phylogenetics
Divisions:	Division of Molecular Biology
Projects:	Project title Project leader Project code Project type Filostratigrafija nastanka i gubitka gena-PhyLoss Tomislav Domazet-Lošo IP-2016-06-5924 HRZZ Napredne metode i tehnologije u znanosti o podatcima i kooperativnim sustavima-DATACROSS Sven Lončarić; Ivan Petrović; Tomislav Šmuc; Andrej Jokić KK.01.1.1.01.009 EK
Depositing User:	Tomislav Domazet-Lošo
Date Deposited:	08 Jan 2026 08:43
URI:	http://fulir.irb.hr/id/eprint/10733
DOI:	10.1038/s41467-024-47017-w

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