Evo-devo: variations on ancestral themes

Most animals evolved from a common ancestor, Urbilateria, which already had in place the developmental genetic networks for shaping body plans. Comparative genomics has revealed rather unexpectedly that many of the genes present in bilaterian animal ancestors were lost by individual phyla during evolution. Reconstruction of the archetypal developmental genomic tool-kit present in Urbilateria will help to elucidate the contribution of gene loss and developmental constraints to the evolution of animal body plans.     

PERSPECTIVE: FROM MUTANTS TO MECHANISMS? ASSESSING THE CANDIDATE GENE PARADIGM IN EVOLUTIONARY BIOLOGY

The generation of mutants in model organisms by geneticists and developmental biologists over the last century has occasionally produced phenotypes that are startlingly reminiscent of those seen in other species. Such extreme mutations have generally been dismissed by evolutionary geneticists since the "modern synthesis" as irrelevant to adaptation and speciation. But only in recent years has information on the molecular bases of mutant phenotypes become widely available, and thus work on testing the relevance of such extreme mutations to the generation of phylogenetic diversity has just begun. Here we evaluate whether evolutionary mimics are, in fact, useful for pinpointing the genetic differences that distinguish morphological variants generated during evolution. Examples come from both plants and animals, and range from intraspecific to interordinal taxonomic ranges. The use of mutationally defined candidate genes to predict evolutionary mechanisms has so far been most fruitful in explaining intraspecific variants, where it has been effective in both plants and animals. In several cases these efforts were facilitated or supported by parallel results from quantitative trait loci studies, in which natural alleles controlling continuous variation in developmental model organisms were mapped to mutationally defined genes. However, despite these successes the approach's utility seems to rapidly decay as a function of phylogenetic distance. This suggests that the divergence of developmental genetic systems is great even in closely related organisms and may become intractable at larger distances. We discuss this result in the context of what it teaches us about development, the future prospects of the candidate gene approach, and the historical debate over process in micro- and macroevolution.     

Evolution of the bilaterian germ line: lineage origin and modulation of specification mechanisms

A key focus of evolutionary developmental biology (evo–devo)in recent years has been to elucidate the evolution of developmentalmechanisms as a means of reconstructing the hypothetical lastcommon ancestors of various clades. Prominent among such reconstructionshave been proposals as to the nature of the mysterious "Urbilateria,"originally defined as the last common ancestor of the extantBilateria (protostomes and deuterostomes). Indeed, drawingsof this animal can now be found, as well as detailed informationon the genetics and morphological processes that it used toconstruct its gut, heart, eyes, appendages, segments, and bodyregions. Perhaps surprisingly, however, no explanations haveyet been offered as to how this animal might have achieved thesuccessful reproduction that must have been necessary for itto give rise to those lineages that are ancestral to today'sdiverse clades. The present article examines the comparativedata available to date on the specification of the only cellscontaining the genetic hereditary material, the germ cells,and speculates on the possible evolutionary and developmentalorigin of the Urbilaterian germ line.     

The derived FOXP2 variant of modern humans was shared with Neandertals

Although many animals communicate vocally, no extant creature rivals modern humans in language ability. Therefore, knowing when and under what evolutionary pressures our capacity for language evolved is of great interest. Here, we find that our closest extinct relatives, the Neandertals, share with modern humans two evolutionary changes in FOXP2, a gene that has been implicated in the development of speech and language. We furthermore find that in Neandertals, these changes lie on the common modern human haplotype, which previously was shown to have been subject to a selective sweep. These results suggest that these genetic changes and the selective sweep predate the common ancestor (which existed about 300,000-400,000 years ago) of modern human and Neandertal populations. This is in contrast to more recent age estimates of the selective sweep based on extant human diversity data. Thus, these results illustrate the usefulness of retrieving direct genetic information from ancient remains for understanding recent human evolution.     

Arabidopsis thaliana leaf form evolved via loss of KNOX expression in leaves in association with a selective sweep

Morphological diversity is often caused by altered gene expression of key developmental regulators. However, the precise developmental trajectories through which morphologies evolved remain poorly understood. It is also unclear to what degree genetic changes contributing to morphological divergence were fixed by natural selection. Here we investigate these problems in the context of evolutionary developmental transitions that produced the simple unlobed leaf of the model species Arabidopsis thaliana. We demonstrate that A. thaliana leaf shape likely derived from a more complex lobed ancestral state that persists in extant Arabidopsis species. We also show that evolution of the unlobed leaf form in A. thaliana involved loss of expression of the knotted1-like homeobox gene SHOOTMERISTEMLESS (STM) in leaves and that cis-regulatory divergence contributed to this process. Further, we provide evidence for a selective sweep at the A. thaliana STM locus, indicating that loss of STM expression in A. thaliana leaves may have been fixed by positive selection. In summary, our data provide key information as to when and how the characteristic leaf form of A. thaliana evolved.     

Co-option of an anteroposterior head axis patterning system for proximodistal patterning of appendages in early bilaterian evolution

The enormous diversity of extant animal forms is a testament to the power of evolution, and much of this diversity has been achieved through the emergence of novel morphological traits. The origin of novel morphological traits is an extremely important issue in biology, and a frequent source of this novelty is co-option of pre-existing genetic systems for new purposes (Carroll et al., 2008). Appendages, such as limbs, fins and antennae, are structures common to many animal body plans which must have arisen at least once, and probably multiple times, in lineages which lacked appendages. We provide evidence that appendage proximodistal patterning genes are expressed in similar registers in the anterior embryonic neurectoderm of Drosophila melanogaster and Saccoglossus kowalevskii (a hemichordate). These results, in concert with existing expression data from a variety of other animals suggest that a pre-existing genetic system for anteroposterior head patterning was co-opted for patterning of the proximodistal axis of appendages of bilaterian animals.     

From extant to extinct: locomotor ontogeny and the evolution of avian flight

Evolutionary transformations are recorded by fossils with transitional morphologies, and are key to understanding the history of life. Reconstructing these transformations requires interpreting functional attributes of extinct forms by exploring how similar features function in extant organisms. However, extinct-extant comparisons are often difficult, because extant adult forms frequently differ substantially from fossil material. Here, we illustrate how postnatal developmental transitions in extant birds can provide rich and novel insights into evolutionary transformations in theropod dinosaurs. Although juveniles have not been a focus of extinct-extant comparisons, developing juveniles in many groups transition through intermediate morphological, functional and behavioral stages that anatomically and conceptually parallel evolutionary transformations. Exploring developmental transitions may thus disclose observable, ecologically relevant answers to long puzzling evolutionary questions.     

生命之树与进化模式:导言

One and half centuries ago, Charles Darwin (1859) presented overwhelming evidence and argued that all life on the earth shared common descent, and "from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved". Ernst Haeckel (1886) and several of his contemporaries attempted to trace the pattern of descent among all extant and extinct forms in what Darwin referred to as "the great Tree of Life". Ever since then, systematists and evolutionary biologists have been exploring morphological, cytogenetic, chemical, developmental and molecular characters, and actively developing theories and methods to infer phylogenetic relationships among organisms from these characters. This endeavor has been especially stimulated by the rise of molecular biology and the emergence of computer science over the past 50 years. At the beginning of the 21st century, we are presented with an unprecedented opportunity to reconstruct the entire Tree of Life, and further, to study evolutionary processes and mechanisms in the context of a robust phylogenetic framework.     

Cranial modularity shifts during mammalian evolution

The mammalian skull has been studied as several separate functional components for decades, but the study of modularity is a more recent, integrative approach toward quantitative examination of independent subsets of highly correlated traits, or modules. Although most studies of modularity focus on developmental and genetic systems, phenotypic modules have been noted in many diverse morphological structures. However, few studies have provided empirical data for comparing modules across higher taxonomic levels, limiting the ability to assess the broader evolutionary significance of modularity. This study uses 18-32 three-dimensional cranial landmarks to analyze phenotypic modularity in 106 mammalian species and demonstrates that cranial modularity is generally conserved in the evolution of therian mammals (marsupials and placentals) but differs between therians and monotremes, the two extant subclasses of Mammalia. Within therians, cluster analyses identify six distinct modules, but only three modules display significant integration in all species. Monotremes display only two highly integrated modules. Specific hypotheses of functional and developmental influences on cranial bones were tested. Theoretical correlation matrices for bones were constructed on the basis of shared function, tissue origin, or mode of ossification, and all three of these models are significantly correlated with observed correlation matrices for the mammalian cranium.     

The eye as a replicating and diverging, modular developmental unit

Sparked by new discoveries in developmental genetics, few topics have generated as much debate as eye evolution. This is somewhat surprising because the central controversy is not unique to eyes, but is a general theme of developmental genetics: evolutionarily conserved genes are deployed during the development of highly divergent morphological features. In the case of eyes, this paradox has engendered opposing camps entrenched in what has been termed a ‘scientific war’. One camp highlights conserved genetic features, concluding that eyes stem from an ancestral prototype. The opposing camp emphasizes variation, arguing that some eyes must have recruited the same genes after separate morphological origins. Here, I blur the line between these camps and suggest that eyes have often evolved by replication, perhaps through the ectopic expression of a conserved, modular regulatory cascade to produce serially homologous structures that often diverged during evolution. Therefore, morphologically diverse eyes could stem from a single ancestral prototype, yet also result from multiple morphological origins.     

Evidence for stasis and not genetic piracy in developmental expression patterns of Branchiostoma lanceolatum and Branchiostoma floridae, two amphioxus species that have evolved independently over the course of 200 Myr

Cephalochordates, the most basal extant group in the phylum Chordata, are represented chiefly by about 20 species of the genus Branchiostoma, commonly called amphioxus or lancelets. In recent years, insights into the evolutionary origin of the vertebrates have been gained from molecular genetic studies during the development of three of these amphioxus species (Branchiostoma floridae in North America, Branchiostoma lanceolatum in Europe, and Branchiostoma belcheri in East Asia). In spite of an estimated divergence time of 100-200 Myr among these species, all three are remarkably similar morphologically, and students of amphioxus have tacitly assumed that such resemblances arise during ontogeny from nearly identical networks of developmental genes. We felt that this assumption needed to be reexamined because instances are known--even in comparisons of closely related species--where characters seeming homologous on the basis of morphology actually develop under the control of conspicuously divergent genetic programs (a phenomenon termed "genetic piracy"). In the present work, we tested the hypothesis that morphological similarities reflect strict conservation of developmentally important genes' expression patterns in order to assess whether the developmental genetics of different amphioxus species show evidence of genetic piracy. To these ends, we cloned 18 genes implicated in different developmental functions in B. lanceolatum and compared their gene expression patterns with the known expression patterns of their orthologous genes in B. floridae. We show that, for the most part, conservation of gene expression parallels that of morphology in these two species. We also identified some differences in gene expression, likely reflecting experimental sensitivity, with the exception of Pax1/9, which may result from true developmental specificities in each amphioxus species. Our results demonstrate that morphological conservation reflects stasis in developmental gene expression patterns and find no evidence for genetic piracy. Thus, different species of amphioxus appear to be very similar, not only morphologically, but also in the genetic programs directing the development of their structural features. Moreover, we provide the first catalogue of gene expression data for the European species, B. lanceolatum.     

A molecular model for the evolution of endothermy in the theropod-bird lineage.

Ectothermy is a primitive state; therefore, a shared common ancestor of crocodiles, dinosaurs, and birds was at some point ectothermic. Birds, the extant descendants of the dinosaurs, are endothermic. Neither the metabolic transition within this lineage nor the place the dinosaurs held along the ectothermic-endothermic continuum is defined. This paper presents a conceptual model for the evolution of endothermy in the theropod-bird lineage. It is recognized that other animals (some fish, insects, etc.) are functionally endothermic. However, endothermy in other clades is beyond the scope of this paper, and we address the onset of endothermy in only the theropod/bird clade. The model begins with simple changes in a single gene of a common ancestor, and it includes a series of concomitant physiological and morphological changes, beginning perhaps as early as the first archosaurian common ancestor of dinosaurs and crocodiles. These changes continued to accumulate within the theropod-avian lineage, were maintained and refined through selective forces, and culminated in extant birds. Metabolic convergence or homoplasy is evident in the inherent differences between the endothermy of mammals and the endothermy of extant birds. The strength and usefulness of this model lie in the phylogenetic, genetic, evolutionary, and adaptive plausibility of each of the suggested developmental steps toward endothermy. The model, although conceptual in nature, relies on an extensive knowledge base developed by numerous workers in each of these areas. In addition, the model integrates known genetic, metabolic, and developmental aspects of extant taxa that phylogenetically bracket theropod dinosaurs for comparison with information derived from the fossil record of related extinct taxa.     

The evolution of plant development

The last decade has witnessed a resurgence in the study of the evolution of plant development, combining investigations in systematics, developmental morphology, molecular developmental genetics, and molecular evolution. The integration of phylogenetic studies, structural analyses of fossil and extant taxa, and molecular developmental genetic information allows the formulation of explicit and testable hypotheses for the evolution of morphological characters. These comprehensive approaches provide opportunities to dissect the evolution of major developmental transitions among land plants, including those associated with apical meristems, the origins of the root/shoot dichotomy, diversification of leaves, and origin and subsequent modification of flower structure. The evolution of these major developmental innovations is discussed within both phylogenetic and molecular genetic contexts. We conclude that it is the combination of these approaches that will lead to the greatest understanding of the evolution of plant development.     

Examining affinities of the Taung child by developmental simulation

As a well-preserved juvenile and the type specimen of Australopithecus africanus, the Taung child figures prominently in taxonomic, ontogenetic, and phylogenetic analyses of fossil hominins. Despite general agreement about allocation of Sterkfontein and Makapansgat fossils to this species, limited morphological comparisons have been possible between these adult specimens and the juvenile Taung. Here, we used developmental simulation to estimate the adult form of the Taung child, and directly compare its morphology to that of other fossil hominins. Specimens were represented by 50 three-dimensional landmarks superimposed by generalized Procrustes analysis. The simulation process applied developmental trajectories from extant hominine species to the Taung fossil in order to generate its adult form. Despite differences found in the developmental patterns of these modern species, simulations tested on extant juveniles-transforming them into "adults" using trajectories from other species-revealed that these differences have negligible impact on adult morphology. This indicates that morphology already present by occlusion of the first permanent molar is the primary determinant of adult form, thereby supporting use of extant trajectories to estimate the morphology of an extinct species. The simulated Taung adult was then compared to other adult fossils. As these comparisons required assumptions about the pattern and magnitude of developmental change, additional analyses were performed to evaluate these two parameters separately. Results of all analyses overwhelmingly rejected the possibility that the Taung child was a juvenile robust australopith, but were consistent with the hypothesis that the Taung and Sterkfontein fossils are conspecific. Between Sts 5 and Sts 71, the latter is more likely to resemble the adult form of the Taung child.     

Temperature-sensitive developmental mutants of Caenorhabditis elegans

About 200 temperature-sensitive mutants of the nematode Caenorhabditis elegans have been isolated. At restrictive temperature, the mutants are blocked in the reproductive life cycle. They have been placed into six broad categories based on their defective phenotypes. The six categories are: (1) mutants blocked in embryogenesis; (2) mutants defective in gonadogenesis; (3) mutants defective in spermatogenesis; (4) mutants that accumulate at an intermediate growth stage; (5) mutants that produce sterile adult progeny; (6) mutants that have a temperature-sensitive morphological defect that interrupts the reproductive life cycle. The critical times of temperature sensitivity have been measured using temperature-shift experiments. Most of the gonadogenesis and spermatogenesis mutants are temperature sensitive during the period of cellular differentiation rather than proliferation. The temperature responses of the gonadogenesis and zygote-defective mutants indicate a common association between functions in gonadogenesis and early embryogenesis. Many of the mutants placed in different categories share other temperature-sensitive phenotypes upon close examination. This implies that many of the functions required for development are general metabolic reactions under increased demand during differentiation and embryogenesis.     

Reorganization of the sex-determining pathway with the evolution of placentation

In mammals, the sex determination system has already been unraveled in considerable detail, and the genes involved are increasingly used to investigate this system in non-mammalian vertebrates. Data available so far indicate that many of the genes identified are involved in this pathway throughout the vertebrate phylum, suggesting that the mechanism of sex determination was essentially conserved in this taxonomic category. However, a rather fundamental difference between mammals and non-mammalian vertebrates is the role of steroid sex hormones which are critical for gonadal differentiation in the latter, while during mammalian evolution an innovation occurred, whereby genes that superseded steroids as factors acting in early gonadogenesis were co-opted to the pathway. An intermediate stage of this evolutionary switch may still be represented by extant marsupials. Referring to the central role of aromatase in steroid-mediated, and of SRY in eutherian gonadal determination/differentiation, it is argued here that the "aromatase system" was replaced by the "SRY system" as a prerequisite for the evolution of placentation. It is proposed that in co-evolution with placentation, new specificities and extensions of the pleiotropic spectrum of sex-determining genes have appeared. The evolutionary innovation of placentation may thus have been materialized by reorganization of the sex-determining system whereby genes were recruited at the top of the pathway and genes at the bottom remained rather conservative but became increasingly pleiotropic.     

The Radiata and the evolutionary origins of the bilaterian body plan

The apparent conservation of cellular and molecular developmental mechanisms observed in a handful of bilaterian metazoans has spawned a "race" to reconstruct the bilaterian ancestor. Knowledge of this ancestor would permit us to reconstruct the evolutionary changes that have occurred along specific bilaterian lineages. However, comparisons among extant bilaterians provide an unnecessarily limited view of the ancestral bilaterian. Since the original bilaterians are believed by many to be derived from a radially symmetrical ancestor, additional evidence might be obtained by examining present-day radially symmetrical animals. We briefly review pertinent features of the body plans of the extant radial eumetazoan phyla, the Cnidaria, and Ctenophora, in the context of revealing potential evolutionary links to the bilaterians.     

The evolutionary origin of developmental enhancers in vertebrates: Insights from non-model species

How random DNA mutations have established the diverse morphology of extant vertebrates is one of the major challenges in evolutionary biology. Thanks to the recent advancement in DNA sequencing technologies, the genome sequences of many non-model species have been determined, which allows us to address previously inaccessible questions about gene regulatory evolution in vertebrates. In particular, the genome sequences of non-teleost ray-finned fishes and cartilaginous fishes offer clues about when and how vertebrates gained developmental enhancers related to morphological traits that were required for the water-to-land transition. In this review, I examine the evolutionary origin of conserved non-coding elements (CNEs), which often function as tissue-specific developmental enhancers, and discuss how CNEs are related to gene regulatory changes that caused the major morphological transitions of vertebrates.     

Signal processing by protein tyrosine phosphorylation in plants

Protein phosphorylation is a reversible post-translational modification controlling many biological processes. Most phosphorylation occurs on serine and threonine, and to a less extend on tyrosine (Tyr). In animals, Tyr phosphorylation is crucial for the regulation of many responses such as growth or differentiation. Only recently with the development of mass spectrometry, it has been reported that Tyr phosphorylation is as important in plants as in animals. The genes encoding protein Tyr kinases and protein Tyr phosphatases have been identified in the Arabidopsis thaliana genome. Putative substrates of these enzymes, and thus Tyr-phosphorylated proteins have been reported by proteomic studies based on accurate mass spectrometry analysis of the phosphopeptides and phosphoproteins. Biochemical approaches, pharmacology and genetic manipulations have indicated that responses to stress and developmental processes involve changes in protein Tyr phosphorylation. The aim of this review is to present an update on Tyr phosphorylation in plants in order to better assess the role of this post-translational modification in plant physiology.Key words: protein tyrosine phosphorylation, kinases, phosphatases, proteomics, mass spectrometry, signaling     

早期胚胎的发育选择:性别决定

性别决定是一个复杂的发育调控过程, 早期胚胎发育过程中, 雌雄二者必居其一的发育选择是胚胎性腺形成必须的发育决定。文章综述了动物性别决定的遗传系统、性腺发生、性别决定关键基因及其作用机制, 从分子进化的角度分析了性染色体与性别决定形成机制, 提示性别决定基因在进化中总是趋向异配性染色体。