On the Possibility of Constructive Neutral Evolution

Stoltzfus, Arlin

doi:10.1007/pl00006540

Cited by 445 publications

(405 citation statements)

References 89 publications

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“…Both developmental bias and niche construction impose directionality on evolution, partly because developmental mechanisms have been shaped by prior selection [73], but also because, like other exploratory behaviour within the organism, learning allows organisms to generate and refine novel behavioural variants that are coherent and adaptive [73,118]. Other types of bias may also affect variation and selection, such as systematic biases in mutation [25,116,117,[119][120][121], or other historical contingencies, such as learned traditions [66,73].…”

Section: (B) Reciprocal Causationmentioning

confidence: 99%

The extended evolutionary synthesis: its structure, assumptions and predictions

et al. 2015

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Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways-one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the 'extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism-environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology.

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Section: (B) Reciprocal Causationmentioning

confidence: 99%

The extended evolutionary synthesis: its structure, assumptions and predictions

et al. 2015

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“…Under neofunctionalization, one copy retains its ancestral functions, and the other acquires a novel function (1). Under subfunctionalization, mutations damage different functions of each copy, such that both copies are required to preserve all ancestral gene functions (9,10). Finally, under specialization, subfunctionalization and neofunctionalization act in concert, producing two copies that are functionally distinct from each other and from the ancestral gene (11).…”

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confidence: 99%

Neofunctionalization of young duplicate genes in Drosophila

Assis

Bachtrog

2013

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

191

332

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Gene duplication is a key source of genetic innovation that plays a role in the evolution of phenotypic complexity. Although several evolutionary processes can result in the long-term retention of duplicate genes, their relative contributions in nature are unknown. Here we develop a phylogenetic approach for comparing genome-wide expression profiles of closely related species to quantify the roles of conservation, neofunctionalization, subfunctionalization, and specialization in the preservation of duplicate genes. Application of our method to pairs of young duplicates in Drosophila shows that neofunctionalization, the gain of a novel function in one copy, accounts for the retention of almost twothirds of duplicate genes. Surprisingly, novel functions nearly always originate in younger (child) copies, whereas older (parent) copies possess functions similar to those of ancestral genes. Further examination of such pairs reveals a strong bias toward RNAmediated duplication events, implicating asymmetric duplication and positive selection in the evolution of new functions. Moreover, we show that young duplicate genes are expressed primarily in testes and that their expression breadth increases over evolutionary time. This finding supports the "out-of-testes" hypothesis, which posits that testes are a catalyst for the emergence of new genes that ultimately evolve functions in other tissues. Thus, our study highlights the importance of neofunctionalization and positive selection in the retention of young duplicates in Drosophila and illustrates how duplicates become incorporated into novel functional networks over evolutionary time.G ene duplication produces two copies of an existing gene.Evolutionary theory predicts that functional redundancy of duplicate genes causes one copy to undergo a brief period of relaxed selection after duplication (1). In nearly all cases, this should result in an accumulation of deleterious mutations and pseudogenization of the copy within a few million years (2). However, most sequenced eukaryotic genomes contain many functional duplicates, some of which are hundreds of millions of years old (3-8), suggesting that duplicate genes play important roles in evolution.Four processes can result in the evolutionary preservation of duplicate genes: conservation, neofunctionalization, subfunctionalization, and specialization. Under conservation, ancestral functions are maintained in both copies, likely because increased gene dosage is beneficial (1). Under neofunctionalization, one copy retains its ancestral functions, and the other acquires a novel function (1). Under subfunctionalization, mutations damage different functions of each copy, such that both copies are required to preserve all ancestral gene functions (9, 10). Finally, under specialization, subfunctionalization and neofunctionalization act in concert, producing two copies that are functionally distinct from each other and from the ancestral gene (11). Theoretical work has shown that different conditions can result in the retention of...

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“…The IL notion that spliceosomal introns as well as the spliceosoma evolved through subfunctionalization of one or more self-splicing group II introns (2,4,5) has gained credit. Once released from the constraints of self-splicing, spliceosomal introns may have been instrumental in creating a profusion of new eukaryotic genes by exon shuffling (6).…”

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A new Drosophila spliceosomal intron position is common in plants

Tarrı́o¹,

Rodrı́guez-Trelles²,

Ayala³

2003

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

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The 25-year-old debate about the origin of introns between proponents of ''introns early'' and ''introns late'' has yielded significant advances, yet important questions remain to be ascertained. One question concerns the density of introns in the last common ancestor of the three multicellular kingdoms. Approaches to this issue thus far have relied on counts of the numbers of identical intron positions across present-day taxa on the assumption that the introns at those sites are orthologous. However, dismissing parallel intron gain for those sites may be unwarranted, because various factors can potentially constrain the site of intron insertion. Demonstrating parallel intron gain is severely handicapped, because intron sequences often evolve exceedingly fast and intron phylogenetic distributions are usually ambiguous, such that alternative loss and gain scenarios cannot be clearly distinguished. We have identified an intron position that was gained independently in animals and plants in the xanthine dehydrogenase gene. The extremely disjointed phylogenetic distribution of the intron argues strongly for separate gain rather than recurrent loss. If the observed phylogenetic pattern had resulted from recurrent loss, all observational support previously gathered for the introns-late theory of intron origins based on the phylogenetic distribution of introns would be invalidated.S pliceosomal introns are one of the hallmarks of eukaryotic genomes, which are distinctively elusive at providing unmixed clues about their evolutionary origins. Yet, after 25 years of contention (see ref. 1 and references therein), the dispute about the origins of introns between ''introns-early'' (IE, alternatively known as the exon theory of genes) and ''introns-late'' (IL) advocates seems to be approaching a synthesis. It is now almost certain that, if the progenote had introns, those could be type II self-splicing introns but never spliceosomal introns (1, 2). Because of the presumably severe constraints imposed on intronic recombination by the role that self-splicing introns play in their own removal, the IE advocates claim that exon shuffling as a factor for the assemblage of primordial genes seems unlikely. However, recent findings in the deeply diverging, putative basal eukaryote Giardia strongly indicate that spliceosomal introns originated in the eukaryotic stem before the diversification of protists, considerably earlier than suggested initially by IL advocates (i.e., around the time of origin of multicellularity; ref.3). The IL notion that spliceosomal introns as well as the spliceosoma evolved through subfunctionalization of one or more self-splicing group II introns (2, 4, 5) has gained credit. Once released from the constraints of self-splicing, spliceosomal introns may have been instrumental in creating a profusion of new eukaryotic genes by exon shuffling (6). IE supporters now admit that intron insertion is an important process in the evolution of eukaryotic genes, although they persist in asserting that deletion of ancest...

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On the Possibility of Constructive Neutral Evolution

Cited by 445 publications

References 89 publications

The extended evolutionary synthesis: its structure, assumptions and predictions

The extended evolutionary synthesis: its structure, assumptions and predictions

Neofunctionalization of young duplicate genes in Drosophila

A new Drosophila spliceosomal intron position is common in plants

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