Nothing in Evolution Makes Sense Except in the Light of Genomics: Read–Write Genome Evolution as an Active Biological Process

Shapiro, James A.

doi:10.3390/biology5020027

Cited by 22 publications

(16 citation statements)

References 393 publications

(445 reference statements)

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“…Indeed, the tree of life has been mocked as the "tree of 1%" (77). A very significant amount of cross-lineage transfer occurs in biological evolution, especially in microbes (78). Mallet (79) estimated that there is hybridization in ∼10% of animal and 25% of plant species.…”

Section: Statedmentioning

confidence: 99%

Cultural macroevolution matters

Gray

Watts

2017

Proc. Natl. Acad. Sci. U.S.A.

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Evolutionary thinking can be applied to both cultural microevolution and macroevolution. However, much of the current literature focuses on cultural microevolution. In this article, we argue that the growing availability of large cross-cultural datasets facilitates the use of computational methods derived from evolutionary biology to answer broad-scale questions about the major transitions in human social organization. Biological methods can be extended to human cultural evolution. We illustrate this argument with examples drawn from our recent work on the roles of Big Gods and ritual human sacrifice in the evolution of large, stratified societies. These analyses show that, although the presence of Big Gods is correlated with the evolution of political complexity, in Austronesian cultures at least, they do not play a causal role in ratcheting up political complexity. In contrast, ritual human sacrifice does play a causal role in promoting and sustaining the evolution of stratified societies by maintaining and legitimizing the power of elites. We briefly discuss some common objections to the application of phylogenetic modeling to cultural evolution and argue that the use of these methods does not require a commitment to either gene-like cultural inheritance or to the view that cultures are like vertebrate species. We conclude that the careful application of these methods can substantially enhance the prospects of an evolutionary science of human history. cultural evolution | macroevolution | phylogenetics | religion | Big Gods D arwin's On the Origin of the Species ends with the poetic phrase, "From so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved" (1). The central challenge for evolutionary biology is to explain this diversity of endless forms. Evolutionary biologists tackle this task by studying both microevolution (changes in gene frequency within a population) and macroevolution (changes between species over much longer time periods). The aim is to have a mechanistic understanding of the evolution of biological diversity that integrates microlevel processes and macrolevel patterns. This work examines ways in which evolutionary thinking and methods can be extended into the realm of culture, extending the scope of biology to include questions that have traditionally been restricted to the humanities and social sciences. Human cultures also display a vast variety of most beautiful and most wonderful forms. We speak ∼7,000 different languages, engage in hundreds of different religious practices, build many different types of houses, exploit different resources for subsistence, use numerous different kinship systems, and abide by a striking array of marital, sexual, and child-rearing norms (2). The cultural processes that produce such striking cultural diversity must be explained. The field of cultural evolution is currently beginning to blossom (Fig. 1). There is a new cultural evolution society, a proposed journal, and an inaugural conference (3). However,...

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Section: Statedmentioning

confidence: 99%

Cultural macroevolution matters

Gray

Watts

2017

Proc. Natl. Acad. Sci. U.S.A.

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“…Much of the relevant information will appear in lists and tables that have two objectives: (1) To make the primary literature accessible to the reader, and (2) to manifest how extensive the literature has become verifying that genome change in evolution results from a series of active biological processes, not from passive accidents. Previous reviews have summarized the outline of the basic arguments presented below [ 10 , 11 , 12 ], but this article presents each topic in greater depth and detail than earlier publications.…”

Section: Introduction and Goalsmentioning

confidence: 99%

Living Organisms Author Their Read-Write Genomes in Evolution

Shapiro

2017

Biology

Self Cite

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Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with “non-coding” DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called “non-coding” RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.

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“…Indeed, many genes of bacterial origin in eukaryotes were obtained through endosymbiotic events that generated actual mitochondria and chloroplast. Even more, many microbial eukaryotes obtained additional genes through secondary and tertiary eukaryote-eukaryote endosymbiosis events (e.g., [141–143]). This results in a very complex evolutionary history of lower eukaryotes and open the door to multiple events of gain/loss of protein genes and an extensive horizontal gene transfer.…”

Section: Discussionmentioning

confidence: 99%

Diversity and Evolutionary Analysis of Iron-Containing (Type-III) Alcohol Dehydrogenases in Eukaryotes

2016

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BackgroundAlcohol dehydrogenase (ADH) activity is widely distributed in the three domains of life. Currently, there are three non-homologous NAD(P)+-dependent ADH families reported: Type I ADH comprises Zn-dependent ADHs; type II ADH comprises short-chain ADHs described first in Drosophila; and, type III ADH comprises iron-containing ADHs (FeADHs). These three families arose independently throughout evolution and possess different structures and mechanisms of reaction. While types I and II ADHs have been extensively studied, analyses about the evolution and diversity of (type III) FeADHs have not been published yet. Therefore in this work, a phylogenetic analysis of FeADHs was performed to get insights into the evolution of this protein family, as well as explore the diversity of FeADHs in eukaryotes.Principal FindingsResults showed that FeADHs from eukaryotes are distributed in thirteen protein subfamilies, eight of them possessing protein sequences distributed in the three domains of life. Interestingly, none of these protein subfamilies possess protein sequences found simultaneously in animals, plants and fungi. Many FeADHs are activated by or contain Fe2+, but many others bind to a variety of metals, or even lack of metal cofactor. Animal FeADHs are found in just one protein subfamily, the hydroxyacid-oxoacid transhydrogenase (HOT) subfamily, which includes protein sequences widely distributed in fungi, but not in plants), and in several taxa from lower eukaryotes, bacteria and archaea. Fungi FeADHs are found mainly in two subfamilies: HOT and maleylacetate reductase (MAR), but some can be found also in other three different protein subfamilies. Plant FeADHs are found only in chlorophyta but not in higher plants, and are distributed in three different protein subfamilies.Conclusions/SignificanceFeADHs are a diverse and ancient protein family that shares a common 3D scaffold with a patchy distribution in eukaryotes. The majority of sequenced FeADHs from eukaryotes are distributed in just two subfamilies, HOT and MAR (found mainly in animals and fungi). These two subfamilies comprise almost 85% of all sequenced FeADHs in eukaryotes.

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Nothing in Evolution Makes Sense Except in the Light of Genomics: Read–Write Genome Evolution as an Active Biological Process

Cited by 22 publications

References 393 publications

Cultural macroevolution matters

Cultural macroevolution matters

Living Organisms Author Their Read-Write Genomes in Evolution

Diversity and Evolutionary Analysis of Iron-Containing (Type-III) Alcohol Dehydrogenases in Eukaryotes

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