Why do we descend from bacteria?

This article examines eukaryogenesis as a major evolutionary transition, focusing on how functional integration enables the emergence of a new biological individual.

Introduction: major evolutionary transitions and eukaryogenesis

The history of life is characterized by the emergence of new organisms that have evolved from their ancestors through natural selection and adaptation. The term "major transitions in evolution" was coined in 1995 by biologists John Maynard Smith and Eörs Szathmáry to describe specific periods in the history of life during which biological organisations undergo radical transformations, leading to the emergence of new living entities (Maynard Smith and Szathmáry 1995).

Major transitions in evolution are characterised by an increase in complexity that “depended on a small number of major transitions in the way in which genetic information is transmitted between generations” (Maynard Smith and Szathmáry 1995, p. 3). Some of these transitions, such as eukaryogenesis and the origin of meiotic sex, occurred once, whereas others, like the origin of multicellularity and animal societies, happened independently multiple times.

Eukaryotic cells are the type of cells found in algae, plants, and animals. As humans, we are composed of eukaryotic cells. Prokaryotic cells, by contrast, are found in bacteria and archaea. Eukaryogenesis refers to the evolutionary origin of eukaryotic cells through a progressive transformation of prokaryotic ancestors. In this sense, we can say that we ultimately derive from prokaryotic life forms.

Eukaryogenesis is considered a major evolutionary transition because it involves a dramatic change in the structural and functional organisation of prokaryotic cells, which include Bacteria and Archaea. The appearance of eukaryotic cells led to an increase in complexity and the emergence of a completely new kind of biological individual (see Fig. 1). Although the main features of prokaryotes, such as the cell membrane, flagella, ribosomes, cytoplasm, and cytoskeleton, are still present in eukaryotes, they have undergone extensive modifications.

Figure 1 (Militello 2025, p. 70)

Eukaryogenesis as a conundrum

Eukaryogenesis remains a major scientific puzzle, with multiple competing hypotheses but no definitive explanation. The term eukaryogenesis refers to the extended evolutionary interval between the first eukaryotic common ancestor (FECA) and the last eukaryotic common ancestor (LECA). The scarcity of proto-eukaryotic fossils, together with the absence of living intermediate forms between prokaryotes and eukaryotes, makes it extremely difficult to determine when eukaryotic cells first emerged.

Although still debated, current estimates suggest that FECA arose between 2.7 and 1.8 billion years ago, while LECA dates to around 1.2 billion years ago (Javaux 2007; Eme et al. 2014). Despite these uncertainties, evolutionary biologists broadly agree that eukaryotic cells originated through the transformation of prokaryotic ancestors.

One of the earliest theories of eukaryogenesis was proposed by Konstantin Mereschkowsky in 1910. He suggested that the eukaryotic nucleus arose through an endosymbiotic relationship between a mycoplasma (the symbiont) and an amoeboid host cell. Endosymbiosis refers to a process in which one organism lives inside another. For several decades, this idea was largely dismissed.

Interest in endosymbiosis was revived in 1967 by Lynn Margulis (then Lynn Sagan), who argued that eukaryotic cells originated through a symbiotic fusion between distinct species (Sagan 1967). This hypothesis was supported by evidence that mitochondria contain their own DNA and replicate independently within the cell. Margulis further noted that many mitochondrial genes are of bacterial origin, pointing to a shared evolutionary ancestry between mitochondria and bacteria.

The precise sequence of events leading to LECA remains uncertain. A range of theoretical models has been proposed, reflecting a pluralistic and multifaceted understanding of the processes underlying eukaryogenesis.

Three theories to explain eukaryogenesis

The theoretical models of eukaryogenesis can be divided into three main groups (see Fig. 2) based on the mechanisms involved in the emergence of the eukaryotic nucleus and whether the nucleus appeared before or after the mitochondria.

The first group comprises the endosymbiotic models (Lake and Rivera 1994; Golding and Gupta 1995; Moreira and Lopez-Garcia 1998; Margulis et al. 2000; Horiike et al. 2004; Forterre 2011; López-García and Moreira 2020), which propose that the nucleus has an endosymbiotic origin.

The second category includes the autogenous models (Taylor 1976; Cavalier-Smith 1988; 2010; Martin and Koonin 2006), which strongly dispute the endosymbiotic origin of the nucleus, asserting that it was an autogenous process resulting from the invagination of the plasma membrane of the proto-eukaryotic cell.

Finally, the third class encompasses the inside-out model (Baum and Baum 2014), according to which the first event in eukaryogenesis was the acquisition of mitochondria. In this model, mitochondria were not endosymbionts, but rather ectosymbionts¹ that were engulfed through protrusions outside the cell wall of the proto-eukaryotic cell. The nucleus is thought to have appeared through an autogenous process following the acquisition of mitochondria.

Interestingly, none of these models offers a definitive account of the temporal sequence of eukaryogenesis: they can consider mitochondria as the initial event, followed by the appearance of the nucleus and all other organelles, or, alternatively, explain the appearance of the nucleus as the earliest event, followed by the development of the endomembranous system and mitochondria/plastids as a later event.

Figure 2 (Militello 2025, p. 78)

Biological Individuality and autonomy in eukaryogenesis

Biological individuality is central to the concept of eukaryogenesis, as it involves the transformation of one form of individual (the prokaryotic cell) into a fundamentally new one. On the one hand, there is significant continuity between these two forms, evidenced by the retention (albeit with modifications) of prokaryotic structures and functions, and the presence of numerous genes of prokaryotic origin in eukaryotes. On the other hand, the emergence of a radically new biological architecture and new functional properties signifies a pivotal shift in the evolution of life. This break in continuity compels us to examine how a physiological and evolutionary individual emerged during eukaryogenesis. Specifically, what conditions allowed the proto-eukaryotic cell to evolve into both a physiological unit and a unit of selection?

Interestingly, current theories of eukaryogenesis do not explicitly address how an autonomous biological organisation emerges during major evolutionary transitions. The dominant explanatory strategies in these theories typically focus on the sequence of structural and functional changes that led to the formation of the modern eukaryotic cell. These theories rely on phylogenetic evidence and hypotheses about the probability of various evolutionary events rather than explicitly connecting these transitions to concepts of biological autonomy. Similarly, Maynard Smith and Szathmáry (1995), while exploring transitions in individuality and complexity, do not directly link these changes to the development of biological autonomy.

Despite this, the models of eukaryogenesis implicitly acknowledge the development of metabolic autonomous capacities and the ability of the eukaryotic cell to interact with and transform its environment. The concept of biological autonomy, therefore, underpins these theories, even if it is not explicitly articulated.

Concluding remarks

Eukaryogenesis offers insights into the origins of physiological and evolutionary individuality and indicates that the development of new structures (such as mitochondria, the endomembrane system, and the cytoskeleton) was accompanied by potential conflicts and challenges. Similarly, the emergence of eukaryotic organelles illuminates the concepts of constitutive and interactive autonomy: the transition from prokaryotic to eukaryotic cells involved the loss of autonomy of the endosymbionts and a significant reorganisation of the host's functional structure. This enabled proto-eukaryotes to develop new methods of self-maintenance and interaction with their environment, thereby fostering new forms of biological autonomy.

The emergence of a new biological individual during eukaryogenesis raises an intriguing question: how is functional integration achieved in such a way as to produce a physiological and autonomous unit with open-ended evolutionary capacities? This major evolutionary transition represents a dramatic shift from one type of functionally integrated organisation to another. The three leading hypotheses on eukaryogenesis propose distinct major changes that contributed to the establishment of a new functionally integrated organisation. These include the endosymbiotic processes leading to the development of mitochondria and the nucleus (as suggested by endosymbiotic theories), the evolution of phagocytosis and the eukaryotic cytoskeleton (as put forward by autogenous models), and the formation of extracellular protrusions that engulfed ectosymbionts (as described by the inside-out model). These changes exerted selective pressures that led to a cascade of events, ultimately resulting in a shift in functional integration.

For more details see Chapter 4 of the Book Functional Integration: A Theoretical Enquiry into the Biological Unit of the Individual.

This article is part of a series on functional integration and biological individuality.

¹Ectosymbionts are organisms living on the surface of another organism.