The origins of microbial adaptations: how introgressive descent, egalitarian evolutionary transitions and expanded kin selection shape the network of life
“…All these complexities became practical problems with the democratization and maturation of genomic methods. For prokaryotes, it was quickly proposed that networks, rather than bifurcating phylogenies, might better describe the evolution of species due to a generally high frequency of HGT [7,8]. The more philosophically minded made the case that the prevalence of HGT was high enough to even question the whole concept of tree-like evolution in prokaryotes, or indeed the existence of a tree of life [9,10].…”
Section: Introduction: the Tree Of Life Conceptmentioning
Developing a detailed understanding of how all known forms of life are related to one another in the tree of life has been a major preoccupation of biology since the idea of tree-like evolution first took hold. Since most life is microbial, our intuitive use of morphological comparisons to infer relatedness only goes so far, and molecular sequence data, most recently from genomes and transcriptomes, has been the primary means to infer these relationships. For prokaryotes this presented new challenges, since the degree of horizontal gene transfer led some to question the tree-like depiction of evolution altogether. Most eukaryotes are also microbial, but in contrast to prokaryotic life, the application of large-scale molecular data to the tree of eukaryotes has largely been a constructive process, leading to a small number of very diverse lineages, or 'supergroups'. The tree is not completely resolved, and contentious problems remain, but many well-established supergroups now encompass much more diversity than the traditional kingdoms. Some of the most exciting recent developments come from the discovery of branches in the tree that we previously had no inkling even existed, many of which are of great ecological or evolutionary interest. These new branches highlight the need for more exploration, by high-throughput molecular surveys, but also more traditional means of observations and cultivation.
“…All these complexities became practical problems with the democratization and maturation of genomic methods. For prokaryotes, it was quickly proposed that networks, rather than bifurcating phylogenies, might better describe the evolution of species due to a generally high frequency of HGT [7,8]. The more philosophically minded made the case that the prevalence of HGT was high enough to even question the whole concept of tree-like evolution in prokaryotes, or indeed the existence of a tree of life [9,10].…”
Section: Introduction: the Tree Of Life Conceptmentioning
Developing a detailed understanding of how all known forms of life are related to one another in the tree of life has been a major preoccupation of biology since the idea of tree-like evolution first took hold. Since most life is microbial, our intuitive use of morphological comparisons to infer relatedness only goes so far, and molecular sequence data, most recently from genomes and transcriptomes, has been the primary means to infer these relationships. For prokaryotes this presented new challenges, since the degree of horizontal gene transfer led some to question the tree-like depiction of evolution altogether. Most eukaryotes are also microbial, but in contrast to prokaryotic life, the application of large-scale molecular data to the tree of eukaryotes has largely been a constructive process, leading to a small number of very diverse lineages, or 'supergroups'. The tree is not completely resolved, and contentious problems remain, but many well-established supergroups now encompass much more diversity than the traditional kingdoms. Some of the most exciting recent developments come from the discovery of branches in the tree that we previously had no inkling even existed, many of which are of great ecological or evolutionary interest. These new branches highlight the need for more exploration, by high-throughput molecular surveys, but also more traditional means of observations and cultivation.
“…Adopting a more permissive account of lineage-generating entities can be particularly useful at explaining different types of biological phenomena (Bapteste 2014;Bapteste et al 2012;De Monte and Rainey 2014;Ereshefsky and Pedroso 2015;Corel et al 2016;Dupré and O'Malley 2009). For example, De Monte and Rainey (2014) focus on the earlier stages of the evolution of multicellularity when parent-offspring relations are poorly defined.…”
Nature is replete with borderline cases that fall somewhere between organisms and communities. One broad class of borderline cases are microbial groups partially formed by the aggregation of cells from the environment, such as slime molds and dental plaque. Some have argued that microbial aggregates do not form lineages because microbial aggregates can acquire cells from the surrounding environment. Nevertheless, Haber (2016) has recently suggested that microbial aggregates may form lineages, but he does not fully elaborate his position. This paper argues that Haber's suggestion is correct as long as a permissive criterion of what constitutes a 'lineage-generating entity' is adopted. Different mechanisms for lineage formation in microbial aggregates will be described to motivate this argument. Unlike mammals, lineage formation in microbial aggregates is more dependent on ecological factors and does not produce well-defined parent-offspring relations. Yet, focusing on the formation of incipient lineages has the benefit of improving our understanding of the processes that hold microbial aggregates together, and it helps bridge the gap between the literature on biological individuality and recent work on microbial communities.
“…Microbiology has gone a long way toward unraveling these processes since its heyday of pure culture studies, a fruitful reductionist approach now complemented by environmental studies. These latter further unraveled that cells compete and cooperate with, and even compensate for each other, within mono- or multispecific microbiomes [ 63 , 64 ]. Both types of microbiomes have a fundamental commonality: they produce collective properties and co-constructed phenotypes (Fig.…”
Section: Biology Is Regulated By Networkmentioning
confidence: 99%
“…Finally, interacting replicated components can be further classified into fraternal components when they share a close last common ancestor (e.g. in kin selection cases), and egalitarian components, when they belong to distinct lineages (as an example, think of the evolution of chimeric genes by fusion and shuffling [ 29 , 45 , 126 ]) [ 63 ]. Fig.…”
Section: Reframing Evolutionary Explanations From the Scaffolded Evolmentioning
The classic Darwinian theory and the Synthetic evolutionary theory and their linear models, while invaluable to study the origins and evolution of species, are not primarily designed to model the evolution of organisations, typically that of ecosystems, nor that of processes. How could evolutionary theory better explain the evolution of biological complexity and diversity? Inclusive network-based analyses of dynamic systems could retrace interactions between (related or unrelated) components. This theoretical shift from a Tree of Life to a Dynamic Interaction Network of Life, which is supported by diverse molecular, cellular, microbiological, organismal, ecological and evolutionary studies, would further unify evolutionary biology.
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