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A central topic in research at the intersection of development and evolution is the origin of novel traits. Despite progress on understanding how developmental mechanisms underlie patterns of diversity in the history of life, the problem of novelty continues to challenge researchers. Here we argue that research on evolutionary novelty and the closely associated phenomenon of co-option can be reframed fruitfully by: (1) specifying a conceptual model of mechanisms that underwrite character identity, (2) providing a richer and more empirically precise notion of co-option that goes beyond common appeals to "deep homology", and (3) attending to the nature of experimental interventions that can determine whether and how the co-option of identity mechanisms can help to explain novel character origins. This reframing has the potential to channel future investigation to make substantive progress on the problem of evolutionary novelty. To illustrate this potential, we apply our reframing to two case studies: treehopper helmets and beetle horns. [ABSTRACT FROM AUTHOR]

Highlights: Details the important contributions and significance of this edited volume for the field.Describes key conceptual questions that remain outstanding. [ABSTRACT FROM AUTHOR]

It is widely accepted that stressful conditions can facilitate evolutionary change. The mechanisms elucidated thus far accomplish this with a generic increase in heritable variation that facilitates more rapid adaptive evolution, often via plastic modifications of existing characters. Through scrutiny of different meanings of stress in biological research, and an explicit recognition that stressors must be characterized relative to their effect on capacities for maintaining functional integrity, we distinguish between: (1) previously identified stress‐responsive mechanisms that facilitate evolution by maintaining an adaptive fit with the environment, and (2) the co‐option of stress‐responsive mechanisms that are specific to stressors leading to the origin of novelties via compensation. Unlike standard accounts of gene co‐option that identify component sources of evolutionary change, our model documents the cost‐benefit trade‐offs and thereby explains how one mechanism—an immediate response to acute stress—is transformed evolutionarily into another—routine protection from recurring stressors. We illustrate our argument with examples from cell type origination as well as processes and structures at higher levels of organization. These examples suggest a general principle of evolutionary origination based on the capacity to switch between regulatory states related to reproduction and proliferation versus survival and differentiation. [ABSTRACT FROM AUTHOR]

Embryo implantation is a hallmark of the female reproductive biology of eutherian (placental) mammals and does not exist in a sustainable form in any other vertebrate group. Implantation is the initial process that leads to a sustained fetal-maternal unit engendering a complex functional relationship between the mother and the embryo/fetus. The nature of this relationship is often portrayed as one of conflict between an aggressive embryo and a passive or defensive maternal organism. Recent progress in elucidating the evolutionary origin of eutherian pregnancy leads to a different picture. The emerging scenario suggests that the very initial stages in the evolution of embryo implantation required evolutionary changes to the maternal physiology which modified an ancestral generic mucosal inflammation in response to the presence of the embryo into an active embedding process. This "female-first" evolutionary scenario also explains the role of endometrial receptivity in human pregnancy. On the marsupial side, where in most animals the fetal–maternal interaction is short and does not lead to a long term sustainable placentation, the relationship is mutual. In these mammals, uterine inflammation is followed by parturition in short order. The inflammatory signaling pathways, however, are cooperative, i.e. they are performed by both the fetus and the mother and therefore we call this relationship "cooperative inflammation." Based on these discoveries we reconceive the narrative of the maternal–fetal relationship. [ABSTRACT FROM AUTHOR]

It was first noticed 100 years ago that mutations tend to affect more than one phenotypic characteristic, a phenomenon that was called 'pleiotropy'. Because pleiotropy was found so frequently, the notion arose that pleiotropy is 'universal'. However, quantitative estimates of pleiotropy have not been available until recently. These estimates show that pleiotropy is highly restricted and are more in line with the notion of variational modularity than with universal pleiotropy. This finding has major implications for the evolvability of complex organisms and the mapping of disease-causing mutations. [ABSTRACT FROM AUTHOR]

Background: The evolution of invasive placentation in the stem lineage of eutherian mammals entailed resolution of the incompatibility between a semi-allogenic fetus and the maternal immune system. The haemochorial placenta of nine-banded armadillo (Dasypus novemcinctus) is thought to conceal itself from the maternal immune system to some degree by developing inside a preformed blood sinus, with minimal contact with the uterine connective tissue. In the present study, we elucidate the micro-anatomical relationship between fetal and maternal tissue of the nine-banded armadillo using histochemical and immunohistochemical tools. Results: We conclude that the chorio-allantoic villi are separated from the myometrium by a vascular endothelial layer, as previously proposed. However, we also observe that the trophoblast cells establish direct contact with the endometrial stroma on the luminal side of the endometrium by partially replacing the endothelial lining of the sinus. Further, we demonstrate the presence of leukocytes, perhaps entrapped, in the placental fibrinoids at the interface between the intervillous space and the endometrial arcade. Conclusions: The trophoblast of the armadillo invades the uterine tissue to a greater extent than was previously believed. We discuss the implications of this finding for the fetal-maternal immune tolerance. [ABSTRACT FROM AUTHOR]

SUMMARY Feathers are an evolutionary novelty found in all extant birds. Despite recent progress investigating feather development and a revolution in dinosaur paleontology, the relationship of feathers to other amniote skin appendages, particularly reptile scales, remains unclear. Disagreement arises primarily from the observation that feathers and avian scutate scales exhibit an anatomical placode-defined as an epidermal thickening-in early development, whereas alligator and other avian scales do not. To investigate the homology of feathers and archosaur scales we examined patterns of nuclear β-catenin localization during early development of feathers and different bird and alligator scales. In birds, nuclear β-catenin is first localized to the feather placode, and then exhibits a dynamic pattern of localization in both epidermis and dermis of the feather bud. We found that asymmetric avian scutate scales and alligator scales share similar patterns of nuclear β-catenin localization with feathers. This supports the hypothesis that feathers, scutate scales, and alligator scales are homologous during early developmental stages, and are derived from early developmental stages of an asymmetric scale present in the archosaur ancestor. Furthermore, given that the earliest stage of β-catenin localization in feathers and archosaur scales is also found in placodes of several mammalian skin appendages, including hair and mammary glands, we hypothesize that a common skin appendage placode originated in the common ancestor of all amniotes. We suggest a skin placode should not be defined by anatomical features, but as a local, organized molecular signaling center from which an epidermal appendage develops. [ABSTRACT FROM AUTHOR]

Feathers are an evolutionary novelty found in all extant birds. Despite recent progress investigating feather development and a revolution in dinosaur paleontology, the relationship of feathers to other amniote skin appendages, particularly reptile scales, remains unclear. Disagreement arises primarily from the observation that feathers and avian scutate scales exhibit an anatomical placode--defined as an epidermal thickening--in early development, whereas alligator and other avian scales do not. To investigate the homology of feathers and archosaur scales we examined patterns of nuclear β-catenin localization during early development of feathers and different bird and alligator scales. In birds, nuclear β-catenin is first localized to the feather placode, and then exhibits a dynamic pattern of localization in both epidermis and dermis of the feather bud. We found that asymmetric avian scutate scales and alligator scales share similar patterns of nuclear β-catenin localization with feathers. This supports the hypothesis that feathers, scutate scales, and alligator scales are homologous during early developmental stages, and are derived from early developmental stages of an asymmetric scale present in the archosaur ancestor. Furthermore, given that the earliest stage of β-catenin localization in feathers and archosaur scales is also found in placodes of several mammalian skin appendages, including hair and mammary glands, we hypothesize that a common skin appendage placode originated in the common ancestor of all amniotes. We suggest a skin placode should not be defined by anatomical features, but as a local, organized molecular signaling center from which an epidermal appendage develops. [ABSTRACT FROM AUTHOR]

Development introduces structured correlations among traits that may constrain or bias the distribution of phenotypes produced. Moreover, when suitable heritable variation exists, natural selection may alter such constraints and correlations, affecting the phenotypic variation available to subsequent selection. However, exactly how the distribution of phenotypes produced by complex developmental systems can be shaped by past selective environments is poorly understood. Here we investigate the evolution of a network of recurrent nonlinear ontogenetic interactions, such as a gene regulation network, in various selective scenarios. We find that evolved networks of this type can exhibit several phenomena that are familiar in cognitive learning systems. These include formation of a distributed associative memory that can 'store' and 'recall' multiple phenotypes that have been selected in the past, recreate complete adult phenotypic patterns accurately from partial or corrupted embryonic phenotypes, and 'generalize' (by exploiting evolved developmental modules) to produce new combinations of phenotypic features. We show that these surprising behaviors follow from an equivalence between the action of natural selection on phenotypic correlations and associative learning, well-understood in the context of neural networks. This helps to explain how development facilitates the evolution of high-fitness phenotypes and how this ability changes over evolutionary time. [ABSTRACT FROM AUTHOR]

Divergence of serially homologous elements of organisms is a common evolutionary pattern contributing to increased phenotypic complexity. Here, we study the genomic intervals affecting the variational independence of fore- and hind limb traits within an experimental mouse population. We use an advanced intercross of inbred mouse strains to map the loci associated with the degree of autonomy between fore- and hind limb long bone lengths (loci affecting the relationship between traits, relationship quantitative trait loci [rQTL]). These loci have been proposed to interact locally with the products of pleiotropic genes, thereby freeing the local trait from the variational constraint due to pleiotropic mutations. Using the known polymorphisms (single nucleotide polymorphisms [SNPs]) between the parental strains, we characterized and compared the genomic regions in which the rQTL, as well as their interaction partners (intQTL), reside. We find that these two classes of QTL intervals harbor different kinds of molecular variation. SNPs in rQTL intervals more frequently reside in limb-specific cis-regulatory regions than SNPs in intQTL intervals. The intQTL loci modified by the rQTL, in contrast, show the signature of protein-coding variation. This result is consistent with the widely accepted view that protein-coding mutations have broader pleiotropic effects than cis-regulatory polymorphisms. For both types of QTL intervals, the underlying candidate genes are enriched for genes involved in protein binding. This finding suggests that rQTL effects are caused by local interactions among the products of the causal genes harbored in rQTL and intQTL intervals. This is the first study to systematically document the population-level molecular variation underlying the evolution of character individuation. [ABSTRACT FROM PUBLISHER]

Transposable elements (TEs) are known to provide DNA for host regulatory functions, but the mechanisms underlying the transformation of TEs into c/s-regulatory elements are unclear. In humans two TEs--MER20 and MER39--contribute the enhancer/ promoter for decidual prolactin (dPRL), which is dramatically induced during pregnancy. We show that evolution of the strong human dPRL promoter was a multistep process that took millions of years. First, MER39 inserted near MER20 in the primate/rodent ancestor, and then there were two phases of activity enhancement in primates. Through the mapping of causal nucleotide substitutions, we demonstrate that strong promoter activity in apes involves epistasis between transcription factor binding sites (TFBSs) ancestral to MER39 and derived sites. We propose a mode of molecular evolution that describes the process by which MER20/MER39 was transformed into a strong promoter, called "epistatic capture." Epistatic capture is the stabilization of a TFBS that is ancestral but variable in outgroup lineages, and is fixed in the ingroup because of epistatic interactions with derived TFBSs. Finally, we note that evolution of human promoter activity coincides with the emergence of a unique reproductive character in apes, highly invasive placentation. Because prolactin communicates with immune cells during pregnancy, which regulate fetal invasion into maternal tissues, we speculate that ape dPRL promoter activity evolved in response to increased invasiveness of ape fetal tissue. [ABSTRACT FROM AUTHOR]

Transposable elements (TEs) are mobile DNA elements found at high frequency in mammalian genomes. Although these elements are generally perceived as genomic parasites, they have the potential to influence host genome function in many beneficial ways. This article discusses the role TEs have played in the evolution of the placenta and pregnancy in viviparous mammals. Using examples from our own research and the literature, we argue that frequent recruitment of TEs, in particular of retroelements, has facilitated the extreme diversification of tissues at the maternal–fetal interface. We also discuss the mechanisms by which TEs have been recruited for functions during pregnancy. We argue that retroelements are pre-adapted to becoming cis-regulatory elements for host genomes because they need to utilize host regulatory signals for their own life cycle. However, although TEs contain some of the signals necessary for host functions upon insertion, they often require modification before acquiring a biological role in a host tissue. We discuss the process by which one TE was transformed into a promoter for prolactin expression in the endometrium, describing a model for TE domestication called ‘epistatic capture’. [ABSTRACT FROM AUTHOR]

Development and physiology translate genetic variation into phenotypic variation and determine the genotype–phenotype map, such as which gene affects which character (pleiotropy). Any genetic change in this mapping reflects a change in development. Here, we discuss evidence for variation in pleiotropy and propose the selection, pleiotropy and compensation model (SPC) for adaptive evolution. It predicts that adaptive change in one character is associated with deleterious pleiotropy in others and subsequent selection to compensate for these pleiotropic effects. The SPC model provides a unifying perspective for a variety of puzzling phenomena, including developmental systems drift and character homogenization. The model suggests that most adaptive signatures detected in genome scans could be the result of compensatory changes, rather than of progressive character adaptations. [ABSTRACT FROM AUTHOR]

Background: A decrease in maternal serum progesterone (P4) concentrations precedes the onset of labor in most placental mammals. Humans differ by maintaining high levels of P4 throughout birth. Parturition in humans probably includes mechanisms that undercut the pregnancy sustaining function of P4. One attractive hypothesis is the isoform switching hypothesis (ISH). ISH is supported by in vitro evidence that progesterone receptor isoform A (PR-A) inhibits PR-B and that the PR-A/PR-B ratio increases towards term. Materials and methods: Here, we test the hypothesis that isoform switching is an adaptation to high levels of P4 at term, predicting that, in humans, PR-A mediated repression of PR-B is stronger than in mouse. We use reporter assays with human and mouse PRs to detect species differences in the repressive effects of PR-A. Results: We found that human PR-B is less sensitive to repression by human PR-A than mouse PR-B, contrary to our prediction. The difference between human and mouse PR-B sensitivity is most pronounced at PR-A/PR-B ratios typical for the preterm myometrium. Conclusions: Our results are inconsistent with the ISH. We speculate that, instead, the lower sensitivity of human PR-B to PR-A may be relevant for the maintenance of pregnancy at high progesterone levels and increasing PR-A concentrations towards term. [ABSTRACT FROM AUTHOR]

Theory suggests that biological modularity and robustness allow for maintenance of fitness under mutational change, and when this change is adaptive, for evolvability. Empirical demonstrations that these traits promote evolvability in nature remain scant however. This is in part because modularity, robustness, and evolvability are difficult to define and measure in real biological systems. Here, we address whether structural modularity and/or robustness confer evolvability at the level of proteins by looking for associations between indices of protein structural modularity, structural robustness, and evolvability. We propose a novel index for protein structural modularity: the number of regular secondary structure elements (helices and strands) divided by the number of residues in the structure. We index protein evolvability as the proportion of sites with evidence of being under positive selection multiplied by the average rate of adaptive evolution at these sites, and we measure this as an average over a phylogeny of 25 mammalian species. We use contact density as an index of protein designability, and thus, structural robustness. We find that protein evolvability is positively associated with structural modularity as well as structural robustness and that the effect of structural modularity on evolvability is independent of the structural robustness index. We interpret these associations to be the result of reduced constraints on amino acid substitutions in highly modular and robust protein structures, which results in faster adaptation through natural selection. [ABSTRACT FROM AUTHOR]

In this article, an approach to measure fitness is proposed that considers fitness as a measure of competitive ability among phenotypes or genotypes. This approach is based on pairwise competition tests and is related to measures of “utility” in mathematical economics. Extending the results from utility theory it is possible to recover the classical Wrightian fitness measure without reference to models of population growth. A condition, quasi-BTL, similar to the Bradley–Terry–Luce condition of classical utility theory is shown to be necessary for the existence of frequency and context-independent fitness measures. Testing for violations of this quasi-BTL condition can be used to the detect genotype-by-genotype interactions and frequency-dependent fitness. A method for the detection of genotype by environment interactions is proposed that avoids potential scaling artifacts. Furthermore the measurement theoretical approach allows one to derive Wright's selection equation. This shows that classical selection equations are entirely general and exact. It is concluded that measurement theory is able to give definite answers to a number theoretical and practical questions. For instance, this theory identifies the correct scale for measuring gene interaction with respect to fitness and shows that different scales may lead to wrong conclusions. [ABSTRACT FROM AUTHOR]

The long legs and short arms of humans are distinctive for a primate, the result of selection acting in opposite directions on each limb at different points in our evolutionary history. This mosaic pattern challenges our understanding of the relationship of development and evolvability because limbs are serially homologous and genetic correlations should act as a significant constraint on their independent evolution. Here we test a developmental model of limb covariation in anthropoid primates and demonstrate that both humans and apes exhibit significantly reduced integration between limbs when compared to quadrupedal monkeys. This result indicates that fossil hominins likely escaped constraints on independent limb variation via reductions to genetic pleiotropy in an ape-like last common ancestor (LCA). This critical change in integration among hominoids, which is reflected in macroevolutionary differences in the disparity between limb lengths, facilitated selection for modern human limb proportions and demonstrates how development helps shape evolutionary change. [ABSTRACT FROM AUTHOR]

Some proteins, such as homeodomain transcription factors, contain highly conserved regions of sequence. It has recently been suggested that multiple functional domains overlap in the homeodomain, together explaining this high conservation. However, the question remains why so many functional domains cluster together in one relatively small and constrained region of the protein. Here we have modeled an evolutionary mechanism that can produce this kind of clustering: conserved functional domains are displaced from the parts of the molecule that are undergoing adaptive evolution because novel functions generally out-compete conserved functions for control over the identity of amino acid residues. We call this model COAA, for Competition Over Amino Acids. We also studied the evolution of amino acid repeats (a.k.a. homopeptides), which are especially prevalent in transcription factors. Repeats that are encoded by non-homogenous mixtures of synonymous codons cannot be explained by replication slippage alone. Our model provides two explanations for their origin, maintenance, and over-representation in highly conserved proteins. We demonstrate that either competition between multiple functional domains for space within a sequence, or reuse of a sequence for many functions over time, can cause the evolution of amino acid repeats. Both of these processes are characteristic of multifunctional proteins such as homeodomain transcription factors. We conclude that the COAA model can explain two widely recognized features of transcription factor proteins: conserved domains and a tendency to accumulate homopeptides. [ABSTRACT FROM AUTHOR]

Re-evolution of lost complex morphological characters has been proposed for several characters, including insect wings, limbs, eyes in snakes, and digits in lizards, among others. There has also been much interest in whether the transition from oviparity to viviparity is reversible, particularly in squamate reptiles where the transition to viviparity has occurred more times than in any other lineage. Here, we present a phylogenetic analysis of boid snakes based on a concatenated multigene study of all genera of erycines, New and Old World boines, plus other groups thought to be closely related with boines such as monotypic species Calabaria and Casarea. We reconstruct ancestral parity mode on this phylogeny and present statistical evidence that oviparity reevolved in a species of Old World sand boa in the genus Eryx nearly 60 million years after the initial boid transition to viviparity. Remarkably, like other viviparous boas hatchlings of oviparous Eryx lack an egg-tooth providing independent evidence that oviparity is a derived state in these species. [ABSTRACT FROM AUTHOR]

A highly conserved spatio-temporal pattern of cartilage formation reveals that the digits of the bird wing develop from positions that become digits 2, 3, and 4 in other amniotes. However, the morphology of the digits of early birds like Archaeopteryx corresponds to that of digits 1, 2, and 3 of other archosaurs. A hypothesis is that a homeotic “frame-shift” occurred, such that in the bird wing, digits 1, 2, and 3 develop from the embryological positions of digits 2, 3, and 4. Experimental homeotic transformations of single digits are well-documented, but frame-shifts of more than one digit are not. We investigated the pattern of cartilage formation in the development of Cyclopamine-treated wings. When Cyclopamine was applied between stages 18 and 21, morphologies that normally develop from positions 2 and 3 developed from positions 3 and 4. The serial shift of digit identity toward posterior confirms a mechanistic possibility that was previously inferred from the evolutionary history of birds. [ABSTRACT FROM AUTHOR]

While the proposal that large-scale genome expansions occurred early in vertebrate evolution is widely accepted, the exact mechanisms of the expansion-such as a single or multiple rounds of whole genome duplication, bloc chromosome duplications, large-scale individual gene duplications, or some combination of these-is unclear. Gene families with a single invertebrate member but four vertebrate members, such as the Hox clusters, provided early support for Ohno's hypothesis that two rounds of genome duplication (the 2R-model) occurred in the stem lineage of extant vertebrates. However, despite extensive study, the duplication history of the Hox clusters has remained unclear, calling into question its usefulness in resolving the role of large-scale gene or genome duplications in early vertebrates. Here, we present a phylogenetic analysis of the vertebrate Hox clusters and several linked genes (the Hox ''paralogon'') and show that different phylogenies are obtained for Dlx and Col genes than for Hox and ErbB genes. We show that these results are robust to errors in phylogenetic inference and suggest that these competing phylogenies can be resolved if two chromosomal crossover events occurred in the ancestral vertebrate. These results resolve conflicting data on the order of Hox gene duplications and the role of genome duplication in vertebrate evolution and suggest that a period of genome reorganization occurred after genome duplications in early vertebrates. [ABSTRACT FROM AUTHOR]

A long-standing question in evolutionary and developmental biology concerns the relative contribution of cis-regulatory and protein changes to developmental evolution. Central to this argument is which mutations generate evolutionarily relevant phenotypic variation? A review of the growing body of evolutionary and developmental literature supports the notion that many developmentally relevant differences occur in the cis-regulatory regions of protein-coding genes, generally to the exclusion of changes in the protein-coding region of genes. However, accumulating experimental evidence demonstrates that many of the arguments against a role for proteins in the evolution of gene regulation, and the developmental evolution in general, are no longer supported and there is an increasing number of cases in which transcription factor protein changes have been demonstrated in evolution. Here, we review the evidence that cis-regulatory evolution is an important driver of phenotypic evolution and provide examples of protein-mediated developmental evolution. Finally, we present an argument that the evolution of proteins may play a more substantial, but thus far underestimated, role in developmental evolution. [ABSTRACT FROM AUTHOR]

A growing debate in evolutionary and developmental biology concerns the relative contribution of cis-regulatory and protein (particularly transcription factor) changes to developmental evolution. Central to this argument are the perceived conservation of transcription factor functions and the modular architecture of cis-regulatory elements. In this paper, we review recent studies on transcription factor proteins that show that transcription factor genes undergo adaptive evolution and evolve novel functions that contribute to the evolution of development. Furthermore, we review experimental work that shows that transcription factor proteins are modular and can evolve with minimal pleiotropic effects. We conclude that changes in the function of proteins are likely directly contributing to developmental evolution. [Copyright &y& Elsevier]

Evolvability, the ability of populations to adapt, can evolve through changes in the mechanisms determining genetic variation and in the processes of development. Here we construct and evolve a simple developmental model in which the pleiotropic effects of genes can evolve. We demonstrate that selection in a changing environment favors a specific pattern of variability, and that this favored pattern maximizes evolvability. Our analysis shows that mutant genotypes with higher evolvability are more likely to increase to fixation. We also show that populations of highly evolvable genotypes are much less likely to be invaded by mutants with lower evolvability, and that this dynamic primarily shapes evolvability. We examine several theoretical objections to the evolution of evolvability in light of this result. We also show that this result is robust to the presence or absence of recombination, and explore how nonrandom environmental change can select for a modular pattern of variability. [ABSTRACT FROM AUTHOR]

Abstract: Epistasis is the dependency of the effect of a mutation on the genetic background in which it occurs. Epistasis has been widely documented and implicated in the evolution of species barriers and the evolution of genetic architecture. Here we propose a simple model to formalize the idea that epistasis can also lead to co-evolutionary patterns in molecular evolution of interacting genes. This model epistasis is represented by the influence of one gene substitution on the fitness rank of the resident allele at another locus. We assume that increasing or decreasing fitness rank occur equally likely. In simulations we show that this form of epistasis leads to co-evolution in the sense that the length of an adaptive walk between interacting loci is highly correlated. This effect is caused by episodes of elevated rate of evolution in both loci simultaneously. We find that the influence of epistasis on these measures of co-evolutionary dynamics is relatively robust to the details of the model. The main factor influencing the correlation in evolutionary rates is the probability that a substitution will have an epistatic effect, but the strength of epistasis or the asymmetry of the initial fitness ranks of the alleles have only a minor effect. We suggest that covariance in rates of evolution among loci could be used to detect epistasis among loci. [Copyright &y& Elsevier]

A network of interactions is called modular if it is subdivided into relatively autonomous, internally highly connected components. Modularity has emerged as a rallying point for research in developmental and evolutionary biology (and specifically evo–devo), as well as in molecular systems biology. Here we review the evidence for modularity and models about its origin. Although there is an emerging agreement that organisms have a modular organization, the main open problem is the question of whether modules arise through the action of natural selection or because of biased mutational mechanisms. [ABSTRACT FROM AUTHOR]

Abstract: Both experimental as well as sequence evolution evidence suggests that transcription factor binding sites can undergo divergence and turnover even when the transcriptional output remains conserved. Furthermore, it is likely that there exist lineage specific differences in the retention rate of binding sites that make it desirable to estimate the rate of acquisition and decay of transcription factor binding sites from comparative sequence data. In this paper we propose a stochastic, phenomenological model for binding site turnover. For a given genomic region we assume a constant rate of binding site origination λ and a constant per site decay rate of μ. We derived an explicit expression for the conditional probability distribution of the number of binding sites n at time t given n 0 binding sites at t=0. The analytical result was compared to a simulation model and we found that it closely predicts the simulated sequence evolution. We then analyzed a small data set of the number of estrogen response elements (ERE) in mammalian HoxA sequences and showed that the data is broadly consistent with the assumption of a stationary turnover process. A regression of shared EREs over the time since divergence led to an estimate of the half-life time for an ERE in the primate HoxA clusters of about 27Myr, which corresponds to a per site decay rate of and a rate of origination of . We conclude that the model can be used to estimate the rate of binding site turnover from comparative genomic data. [Copyright &y& Elsevier]

Homology is an essential idea of biology, referring to the historical continuity of characters, but it is also conceptually highly elusive. The main difficulty is the apparently loose relationship between morphological characters and their genetic basis. Here I propose that it is the historical continuity of gene regulatory networks rather than the expression of individual homologous genes that underlies the homology of morphological characters. These networks, here referred to as 'character identity networks', enable the execution of a character-specific developmental programme. [ABSTRACT FROM AUTHOR]

Abstract: We study to what degree patterns of amino acid substitution vary between genes using two models of protein-coding gene evolution. The first divides the amino acids into groups, with one substitution rate for pairs of residues in the same group and a second for those in differing groups. Unlike previous applications of this model, the groups themselves are estimated from data by simulated annealing. The second model makes substitution rates a function of the physical and chemical similarity between two residues. Because we model the evolution of coding DNA sequences as opposed to protein sequences, artifacts arising from the differing numbers of nucleotide substitutions required to bring about various amino acid substitutions are avoided. Using 10 alignments of related sequences (five of orthologous genes and five gene families), we do find differences in substitution patterns. We also find that, although patterns of amino acid substitution vary temporally within the history of a gene, variation is not greater in paralogous than in orthologous genes. Improved understanding of such gene-specific variation in substitution patterns may have implications for applications such as sequence alignment and phylogenetic inference. [Copyright &y& Elsevier]

Reevolution of lost characters constitutes evidence that the capacity for producing specific phenotypes may remain latent after a trait is lost and be transmitted over many generations without visible effect. Although some evolutionary changes are easily reversible, it can be argued that the reappearance of complex characters would be nearly impossible. This idea is based on the assumption that, after a structure is lost, the genes related to its development will degenerate. In the present paper we test this idea with respect to digit loss in the gymnophthalmid genus Bachia. We present a molecular phylogeny of the genus Bachia and investigate the evolution of digit number in this taxon. Most members of this South American genus have undergone major reduction in hind limbs without ever losing all the digits in the forelimbs. We apply three statistical methods to test the hypothesis that trail loss is irreversible (Dollo's law). These are tree tests, parsimony cost curves, and likelihood-ratio tests. Data is also analyzed under a simple probability model. All analyses provided strong evidence for reevolution of digit number in derived Bachia species. The evidence is stronger in toes (hind limb) than in fingers (forelimb). Other published examples of reevolution of complex traits are discussed in the light of the statistical approaches used in this paper. We conclude that there are a limited number of cases with strong evidence for the reevolution of lost morphological structures, raising questions about the mechanisms that retain the genetic information for a latent character. [ABSTRACT FROM AUTHOR]

Abstract: The tetrapod limb, which has served as a paradigm for the study of development and morphological evolution, is becoming a paradigm for developmental evolution as well. In its origin and diversification, the tetrapod limb has undergone a great deal of remodeling. These morphological changes and other evolutionary phenomena have produced variation in mechanisms of tetrapod limb development. Here, we review that variation in the four major clades of limbed tetrapods. Comparisons in a phylogenetic context reveal details of development and evolution that otherwise may have been unclear. Such details include apparent differences in the mechanisms of dorsal–ventral patterning and limb identity specification between mouse and chick and mechanistic novelties in amniotes, anurans, and urodeles. As we gain a better understanding of the details of limb development, further differences among taxa will be revealed. The use of appropriate comparative techniques in a phylogenetic context thus sheds light on evolutionary transitions in limb morphology and the generality of developmental models across species and is therefore important to both evolutionary and developmental biologists. [Copyright &y& Elsevier]

Abstract: The identity of avian digits has been unresolved since the beginning of evolutionary morphology in the mid-19th century, i.e. as soon as questions of phylogenetic homology have been raised. The main source of concern is the persistent discrepancy between anatomical/paleontological and embryological evidence over the identity of avian digits. In this paper, recent evidence pertaining to the question of avian digit homology is reviewed and the various ideas of how to resolve the disagreement among developmental and phylogenetic evidence are evaluated. Paleontological evidence unequivocally supports the hypothesis that the fully formed digits of maniraptoran theropods are digits DI, DII, and DIII, because the phylogenetic position of Herrerasaurus is resolved, even when hand characters are excluded from the analysis. Regarding the developmental origin of the three digits of the avian hand the discovery of an anterior digit condensation in the limb bud of chickens and ostriches conclusively shows that these three digits are developing from condensations CII, CIII, and CIV. The existence of this additional anterior condensation has been confirmed in four different labs, using four different methods: Alcian blue staining, PNA affinity histochemistry, micro-capillary regression and Sox9 expression. Finally, recent evidence shows that the digit developing from condensation CII has a Hox gene expression pattern that is found in digit DI of mice forelimb and chick hind limbs. The sum of these data supports the idea that digit identity has shifted relative to the location of condensations, known as Frame Shift Hypothesis, such that condensation CII develops into digit DI and condensation CIII develops into digit DII, etc. A review of the literature on the digit identity of the Italian Three-toed Skink or Luscengola (Chalcides chalcides), shows that digit identity frame shifts may not be limited to the bird hand but may be characteristic of “adaptive” digit reduction in amniotes (sensu Steiner, H., Anders, G., 1946. Zur Frage der Entstehung von Rudimenten. Die Reduktion der Gliedmassen von Chalcides tridactylus Laur. Rev. Suisse Zool. 53, 537–546) in general. In this mode of evolution two digits are lost, in the course of the adaptation of the three anterior digits to a function that does not require the two posterior digits. This evidence suggests that the evolution of digits in tetrapods can proceed at least on two distinct levels of integration, the level of digit condensations and that of adult digits. [Copyright &y& Elsevier]

In this study the molecular evolution of duplicated HoxA genes in zebrafish and fugu has been investigated. All 18 duplicated HoxA genes studied have a higher non-synonymous substitution rate than the corresponding genes in either bichir or paddlefish, where these genes are not duplicated. The higher rate of evolution is not due solely to a higher non-synonymous-to-synonymous rate ratio but to an increase in both the non-synonymous as well as the synonymous substitution rate. The synonymous rate increase can be explained by a change in base composition, codon usage, or mutation rate. We found no changes in nucleotide composition or codon bias. Thus, we suggest that the HoxA genes may experience an increased mutation rate following cluster duplication. In the non-Hox nuclear gene RAG1 only an increase in non-synonymous substitutions could be detected, suggesting that the increased mutation rate is specific to duplicated Hox clusters and might be related to the structural instability of Hox clusters following duplication. The divergence among paralog genes tends to be asymmetric, with one paralog diverging faster than the other. In fugu, all b-paralogs diverge faster than the a-paralogs, while in zebrafish Hoxa-13a diverges faster. This asymmetry corresponds to the asymmetry in the divergence rate of conserved non-coding sequences, i.e., putative cis-regulatory elements. These results suggest that the 5′ HoxA genes in the same cluster belong to a co-evolutionary unit in which genes have a tendency to diverge together. [ABSTRACT FROM AUTHOR]

One of the most solid generalizations of transmission genetics is that the phenotypic variance of populations carrying a major mutation is increased relative to the wild type. At least some part of this higher variance is genetic and due to release of previously hidden variation. Similarly, stressful environments also lead to the expression of hidden variation. These two observations have been considered as evidence that the wild type has evolved robustness against genetic variation, i.e., genetic canalization. In this article we present a general model for the interaction of a major mutation or a novel environment with the additive genetic basis of a quantitative character under stabilizing selection. We introduce an approximation to the genetic variance in mutation-selection-drift balance that includes the previously used stochastic Gaussian and house-of-cards approximations as limiting cases. We then show that the release of hidden genetic variation is a generic property of models with epistasis or genotype-environment interaction, regardless of whether the wild-type genotype is canalized or not. As a consequence, the additive genetic variance increases upon a change in the environment or the genetic background even if the mutant character state is as robust as the wild-type character. Estimates show that this predicted increase can be considerable, in particular in large populations and if there are conditionally neutral alleles at the loci underlying the trait. A brief review of the relevant literature suggests that the assumptions of this model are likely to be generic for polygenic traits. We conclude that the release of hidden genetic variance due to a major mutation or environmental stress does not demonstrate canalization of the wild-type genotype. [ABSTRACT FROM AUTHOR]

Dominance is a form of phenotypic robustness to mutations. Understanding how such robustness can evolve provides a window into how the relation between genotype and phenotype can evolve. As such, the issue of dominance evolution is a question about the evolution of inheritance systems. Attempts at explaining the evolution of dominance have run into two problems. One is that selection for dominance is sensitive to the frequency of heterozygotes. Accordingly, dominance cannot evolve unless special conditions lead to the presence of a high frequency of mutant alleles in the population. Second, on the basis of theoretical results in metabolic control analysis, it has been proposed that metabolic systems possess inherent constraints. These hypothetical constraints imply the default manifestation of dominance of the wild type with respect to the effects of mutations at most loci. Hence, some biologists have maintained that an evolutionary explanation is not relevant to dominance. In this article, we put into question the hypothetical assumption of default metabolic constraints. We show that this assumption is based on an exclusion of important nonlinear interactions that can occur between enzymes in a pathway. With an a priori exclusion of such interactions, the possibility of epistasis and hence dominance modification is eliminated. We present a theoretical model that integrates enzyme kinetics and population genetics to address dominance evolution in metabolic pathways. In the case of mutations that decrease enzyme concentrations, and given the mechanistic constraints of Michaelis-Menten-type catalysis, it is shown that dominance of the wild type can be extensively modified in a two-enzyme pathway. Moreover, we discuss analytical results indicating that the conclusions from the two-enzyme case can be generalized to any number of enzymes. Dominance modification is achieved chiefly through changes in enzyme concentrations or kinetic parameters such as kcat, both of which can alter saturation levels. Low saturation translates into higher levels of dominance with respect to mutations that decrease enzyme concentrations. Furthermore, it is shown that in the two-enzyme example, dominance evolves as a by-product of selection in a manner that is insensitive to the frequency of heterozygotes. Using variation in kcat as an example of modifier mutations, it is shown that the latter can have direct fitness effects in addition to dominance modification effects. Dominance evolution can occur in a frequency-insensitive manner as a result of selection for such dual-effects alleles. This type of selection may prove to be a common pattern for the evolution of phenotypic robustness to mutations. [ABSTRACT FROM AUTHOR]

SUMMARY The capacity to regenerate limbs is very high in amphibians and practically absent in other tetrapods despite the similarities in developmental pathways and ultimate morphology of tetrapod limbs. We propose that limb regeneration is only possible when the limb develops as a semiautonomous module and is not involved in interactions with transient structures. This hypothesis is based on the following two assumptions: To an important extent, limb development uses the same developmental mechanisms as normal limb development and developmental mechanisms that require interactions with transient structures cannot be recapitulated later. In amniotes limb development is early, shortly after neurulation, and requires inductive interactions with transient structures such as somites. In amphibians limb development is delayed relative to amniotes and has become decoupled from interactions with somites and other transient structures that are no longer present at this stage. The limb develops as a semi-independent module. A comparison of the autonomy and timing of limb development in different vertebrate taxa supports our hypothesis and its assumptions. The data suggest a good correlation between self-organizing and regenerative capacity. Furthermore, they suggest that whatever barriers amphibians overcame in the evolution of metamorphosis, they are the same barriers that need to be overcome to make limb regeneration possible in other taxa. [ABSTRACT FROM AUTHOR]

In this paper Lewontin’s notion of “quasi-independence” of characters is formalized as the assumption that a region of the phenotype space can be represented by a product space of orthogonal factors. In this picture each character corresponds to a factor of a region of the phenotype space. We consider any region of the phenotype space that has a given factorization as a “type”, i.e. as a set of phenotypes that share the same set of phenotypic characters. Using the notion of local factorizations we develop a theory of character identity based on the continuation of common factors among different regions of the phenotype space. We also consider the topological constraints on evolutionary transitions among regions with different regional factorizations, i.e. for the evolution of new types or body plans. It is shown that direct transition between different “types” is only possible if the transitional forms have all the characters that the ancestral and the derived types have and are thus compatible with the factorization of both types. Transitional forms thus have to go over a “complexity hump” where they have more quasi-independent characters than either the ancestral as well as the derived type. The only logical, but biologically unlikely, alternative is a “hopeful monster” that transforms in a single step from the ancestral type to the derived type. Topological considerations also suggest a new factor that may contribute to the evolutionary stability of “types”. It is shown that if the type is decomposable into factors which are vertex irregular (i.e. have states that are more or less preferred in a random walk), the region of phenotypes representing the type contains islands of strongly preferred states. In other words types have a statistical tendency of retaining evolutionary trajectories within their interior and thus add to the evolutionary persistence of types. [Copyright &y& Elsevier]

Comments on the lineage ancestral in relation to the morphological innovations of male sepsid flies. Developmental amorphuses of the for ancestral constraint; Scrutiny on the sexual selection associated in the morphological innovations; Phylogenetic characteristics on the evolution of male sepsid flies.

Evolution can be regarded as the exploration of genetic or morphological state space by populations. In traditional models of population and quantitative genetics, the state space can be formally represented as a configuration space with clearly defined concepts of neighborhood and distance, defined by the action of variational operators such as mutation and/or recombination. In this paper, we describe a process where no genetic configuration space closure (and hence, no non-arbitrary notion of distance and neighborhood) exists. The process is gene duplication by means of unequal crossover, which we regard as an example of an “innovation” process that changes the state space of the system rather than exploring a closed state space. We assert that such processes are qualitatively distinct from representations of the adaptation process, which occur on regular configuration spaces. [ABSTRACT FROM AUTHOR]

Morphological novelty has the status of a distinct problem in evolutionary biology. The present understanding of novelty, however, is characterised by remarkable heterogeneity. Empirical approach in the problem of novelty has to focus on the organizational principles of developmental systems and their ability to generate new structures. Even when limited to the morphological level, very different attitudes are taken toward the problem in current evolutionary biology. The prevailing one is a purely phenomenological treatment of novelty.

The article presents a personal narrative relating the experiences of the author as he becomes involved in the field of evolutionary developmental biology (evo-devo).

As perceived by Darwin, evolutionary adaptation by the processes of mutation and selection is difficult to understand for complex features that are the product of numerous traits acting in concert, for example the eye or the apparatus of flight. Typically, mutations simultaneously affect multiple phenotypic characters. This phenomenon is known as pleiotropy. The impact of pleiotropy on evolution has for decades been the subject of formal analysis. Some authors have suggested that pleiotropy can impede evolutionary progress (a so-called ‘cost of complexity’). The plausibility of various phenomena attributed to pleiotropy depends on how many traits are affected by each mutation and on our understanding of the correlation between the number of traits affected by each gene substitution and the size of mutational effects on individual traits. Here we show, by studying pleiotropy in mice with the use of quantitative trait loci (QTLs) affecting skeletal characters, that most QTLs affect a relatively small subset of traits and that a substitution at a QTL has an effect on each trait that increases with the total number of traits affected. This suggests that evolution of higher organisms does not suffer a ‘cost of complexity’ because most mutations affect few traits and the size of the effects does not decrease with pleiotropy. [ABSTRACT FROM AUTHOR]

• The first viviparous mammals likely faced innate, not adaptive, immune constraints on pregnancy duration. • Inflammatory stages of pregnancy were modified through the transfer of a cell-cell communication network between cell types. • Recruitment of inflammation into reproductive physiology likely occurred independently in marsupials and eutherian mammals. • Marsupials modified the ancestral attachment response into cooperative inflammation, fostering rapid growth and parturition. • Eutherians modified the ancestral inflammatory response into embryo implantation, and achieved extended gestation. The evolution of viviparity in therian mammals, i.e. marsupials and "placental" mammals, occurred by retention of the conceptus in the female reproductive tract and precocious "hatching" from the shell coat. Both eutherian embryo implantation and the opossum embryo attachment reaction are evolutionarily derived from and homologous to a defensive inflammatory process induced after shell coat hatching. However, both lineages, marsupials and placental mammals, have modified the inflammatory response substantially. We review the induction, maintenance, and effects of inflammation throughout pregnancy, with special attention to the role of prostaglandins and the mucosal inflammatory response, both of which likely had roles in early mammalian viviparity. We propose that the key step was not only suppression of the inflammatory response after implantation in placental mammals, but also the transfer of the inflammatory cell-cell communication network to a different set of cell types than in generic inflammation. To support this conclusion we discuss evidence that pro-inflammatory signal production in the opossum is not limited to maternal cells, as expected in bona fide defensive inflammation, but also includes fetal tissues, in a process we term cooperative inflammation. The ways in which the inflammatory reaction was independently modified in these two lineages helps explain major life history differences between extant marsupials and eutherians. [ABSTRACT FROM AUTHOR]

The article discusses cellular senescence is a consequence of the second law of thermodynamics, due to mutations, epigenetic misregulation, and protein misfolding. It mentions competition among cells has been killed to ensure cooperation among cells and integrity of the organism. It also mentions breakdown of cooperation and unchecked competition among cells leads to cancer.

Understanding the evolutionary role of environmentally induced phenotypic variation (i.e., plasticity) is an important issue in developmental evolution. A major physiological response to environmental change is cellular stress, which is counteracted by generic stress reactions detoxifying the cell. A model, stress‐induced evolutionary innovation (SIEI), whereby ancestral stress reactions and their corresponding pathways can be transformed into novel structural components of body plans, such as new cell types, is described. Previous findings suggest that the cell differentiation cascade of a cell type critical to pregnancy in humans, the decidual stromal cell, evolved from a cellular stress reaction. It is hypothesized that the stress reaction in these cells was elicited ancestrally via inflammation caused by embryo attachment. The present study proposes that SIEI is a distinct form of plasticity‐based evolutionary change leading to the origin of novel structures rather than adaptive transformation of pre‐existing characters. Cells frequently counteract environmental stress by conserved molecular mechanisms, leading to stress mitigation or apoptosis. Increasingly, studies on cellular stress responses intersect with cell type differentiation programs. It is hypothesized that integration of these conserved pathways is a mechanism of stress‐induced evolutionary innovation that is capable of generating novel cell types. [ABSTRACT FROM AUTHOR]