Leaf adaxial-abaxial polarity specification and lamina outgrowth: evolution and development

A key innovation in leaf evolution is the acquisition of a flat lamina with adaxial-abaxial polarity, which optimizes the primary function of photosynthesis. The developmental mechanism behind leaf adaxial-abaxial polarity specification and flat lamina formation has long been of interest to biologists. Surgical and genetic studies proposed a conceptual model wherein a signal derived from the shoot apical meristem is necessary for adaxial-abaxial polarity specification, and subsequent lamina outgrowth is promoted at the juxtaposition of adaxial and abaxial identities. Several distinct regulators involved in leaf adaxial-abaxial polarity specification and lamina outgrowth have been identified. Analyses of these genes demonstrated that the mutual antagonistic interactions between adaxial and abaxial determinants establish polarity and define the boundary between two domains, along which lamina outgrowth regulators function. Evolutionary developmental studies on diverse leaf forms of angiosperms proposed that alteration to the adaxial-abaxial patterning system can be a major driving force in the generation of diverse leaf forms, as represented by 'unifacial leaves', in which leaf blades have only the abaxial identity. Interestingly, unifacial leaf blades become flattened, in spite of the lack of adaxial-abaxial juxtaposition. Modification of the adaxial-abaxial patterning system is also utilized to generate complex organ morphologies, such as stamens. In this review, we summarize recent advances in the genetic mechanisms underlying leaf adaxial-abaxial polarity specification and lamina outgrowth, with emphasis on the genetic basis of the evolution and diversification of leaves.     

A Role for Auxin in Triggering Lamina Outgrowth of Unifacial Leaves

A common morphological feature of typical angiosperms is the patterning of lateral organs along primary axes of asymmetry—a proximodistal, a mediolateral, and an adaxial–abaxial axis. Angiosperm leaves usually have distinct adaxial–abaxial identity, which is required for the development of a flat shape. By contrast, many unifacial leaves, consisting of only the abaxial side, show a flattened morphology. This implicates a unique mechanism that allows leaf flattening independent of adaxial–abaxial identity. In this study, we report a role for auxin in outgrowth of unifacial leaves. In two closely related unifacial-leaved species of Juncaceae, Juncus prismatocarpus with flattened leaves, and Juncus wallichianus with transversally radialized leaves, the auxin-responsive gene GLYCOSIDE HYDROLASE3 displayed spatially different expression patterns within leaf primordia. Treatment of J. prismatocarpus seedlings with exogenous auxin or auxin transport inhibitors, which disturb endogenous auxin distribution, eliminated leaf flatness, resulting in a transversally radialized morphology. These treatments did not affect the radialized morphology of leaves of J. wallichianus. Moreover, elimination of leaf flatness by these treatments accompanied dysregulated expression of genetic factors needed to specify the leaf central-marginal polarity in J. prismatocarpus. The findings imply that lamina outgrowth of unifacial leaves relies on proper placement of auxin, which might induce initial leaf flattening and subsequently act to specify leaf polarity, promoting further flattening growth of leaves.

Lamina outgrowth of unifacial leaves, which lack adaxial identity, relies on proper localization of auxin, which might induce initial leaf flattening and subsequently act to specify leaf polarity, promoting further flattening growth of leaves.     

COMPARATIVE FOLIAR HISTOGENESIS IN ACORUS CALAMUS AND ITS BEARING ON THE PHYLLODE THEORY OF MONOCOTYLEDONOUS LEAVES

A comparative histogenetic investigation of the unifacial foliage leaves of Acorus calamus L. (Araceae; Pothoideae) was initiated for the purposes of: (1) re-evaluating the previous sympodial interpretation of unifacial leaf development; (2) comparing the mode of histogenesis with that of the phyllode of Acacia in a re-examination of the phyllode theory of monocotyledonous leaves; and (3) specifying the histogenetic mechanisms responsible for morphological divergence of the leaf of Acorus from dorsiventral leaves of other Araceae. Leaves in Acorus are initiated in an orthodistichous phyllotaxis from alternate positions on the bilaterally symmetrical apical meristem. During each plastochron the shoot apex proceeds through a regular rhythm of expansion and reduction related to leaf and axillary meristem initiation and regeneration. The shoot apex has a three- to four-layered tunica and subjacent corpus with a distinctive cytohistological zonation evident to varying degrees during all phases of the plastochron. Leaf initiation is by periclinal division in the second through fourth layers of the meristem. Following inception early growth of the leaf primordium is erect, involving apical and intercalary growth in length as well as marginal growth in circumference in the sheathing leaf base. Early maturation of the leaf apex into an attenuated tip marks the end of apical growth, and subsequent growth in length is largely basal and intercalary. Marked radial growth is evident early in development and initially is mediated by a very active adaxial meristem; the median flattening of this leaf is related to accentuated activity of this meristematic zone. Differentiation of the secondary midrib begins along the center of the leaf axis and proceeds in an acropetal direction. Correlated with this centralized zone of tissue specialization is the first appearance of procambium in the center of the leaf axis. Subsequent radial expansion of the flattened upper leaf zone is bidirectional, proceeding by intercalary meristematic activity at both sides of the central midrib. Procambial differentiation is continuous and acropetal, and provascular strands are initiated in pairs in both sides of the primordium from derivatives of intercalary meristems in the abaxial and adaxial wings of the leaf. Comparative investigation of foliar histogenesis in different populations of Acorus from Wisconsin and Iowa reveals different degrees of apical and adaxial meristematic activity in primordia of these two collections: leaves with marked adaxial growth exhibit delayed and reduced expression of apical growth, whereas primordia with marked apical growth show, correspondingly, reduced adaxial meristematic activity at equivalent stages of development. Such variations in leaf histogenesis are correlated with marked differences in adult leaf anatomy in the respective populations and explain the reasons for the sympodial interpretation of leaf morphogenesis in Acorus and unifacial organs of other genera by previous investigators. It is concluded that leaf development in Acorus resembles that of the Acacia phyllode, thereby confirming from a developmental viewpoint the homology of these organs. Comparison of development with leaves of other Araceae indicates that the modified form of the leaf of Acorus originates through the accentuation of adaxial and abaxial meristematic activity which is expressed only slightly in the more conventional dorsiventral leaf types in the family.     

Evolutionary developmental biology and the problem of variation

Abstract. One of the oldest problems in evolutionary biology remains largely unsolved. Which mutations generate evolutionarily relevant phenotypic variation? What kinds of molecular changes do they entail? What are the phenotypic magnitudes, frequencies of origin, and pleiotropic effects of such mutations? How is the genome constructed to allow the observed abundance of phenotypic diversity? Historically, the neo‐Darwinian synthesizers stressed the predominance of micromutations in evolution, whereas others noted the similarities between some dramatic mutations and evolutionary transitions to argue for macromutationism. Arguments on both sides have been biased by misconceptions of the developmental effects of mutations. For example, the traditional view that mutations of important developmental genes always have large pleiotropic effects can now be seen to be a conclusion drawn from observations of a small class of mutations with dramatic effects. It is possible that some mutations, for example, those in cis‐regulatory DNA, have few or no pleiotropic effects and may be the predominant source of morphological evolution. In contrast, mutations causing dramatic phenotypic effects, although superficially similar to hypothesized evolutionary transitions, are unlikely to fairly represent the true path of evolution. Recent developmental studies of gene function provide a new way of conceptualizing and studying variation that contrasts with the traditional genetic view that was incorporated into neo‐Darwinian theory and population genetics. This new approach in developmental biology is as important for micro‐evolutionary studies as the actual results from recent evolutionary developmental studies. In particular, this approach will assist in the task of identifying the specific mutations generating phenotypic variation and elucidating how they alter gene function. These data will provide the current missing link between molecular and phenotypic variation in natural populations.     

Shoot apex,leaf development and unifacial tip inAgave wightii drumm. et prain (agavaceae)

The shoot apex has one tunica layer enclosing a mass of corpus which is differentiated cytohistologically into central mother cell zone, flank zone, rib zone and a ‘cambium-like’ zone. Occurrence of ‘cambium-like’ zone during minimal phase is considered as an expression of nodal region. Agave wightii shows spirodistichous arrangement of leaves which have an expanded photosynthetic surface with a reduced unifacial tip. Leaves are initiated by periclinal divisions in the second layer. Vertical growth in the leaves is by subapical initials and lateral growth is by marginal and submarginal initials in their early stages of development. The unifacial tip is formed by the extension of adaxial meristematic activity. The derivatives thus formed are pushed to the abaxial side of the primordiuj. Hence the unifacial part of the leaf is regarded as equivalent to a phyllode.     

Speciation and development

Understanding general principles about the origin of species remains one of the foundational challenges in evolutionary biology. The genomic divergence between groups of individuals can spawn hybrid inviability and hybrid sterility, which presents a tantalizing developmental problem. Divergent developmental programs may yield either conserved or divergent phenotypes relative to ancestral traits, both of which can be responsible for reproductive isolation during the speciation process. The genetic mechanisms of developmental evolution involve cis- and trans-acting gene regulatory change, protein–protein interactions, genetic network structures, dosage, and epigenetic regulation, all of which also have roots in population genetic and molecular evolutionary processes. Toward the goal of demystifying Darwin's “mystery of mysteries,” this review integrates microevolutionary concepts of genetic change with principles of organismal development, establishing explicit links between population genetic process and developmental mechanisms in the production of macroevolutionary pattern. This integration aims to establish a more unified view of speciation that binds process and mechanism.     

花、基因、禾本科

进化发育生物学的一个重要任务就是揭示形态多样性的分子基础,该领域的研究包含形态、形态发育相关基因和形态所属类群等三个要素。花/花序是进化发育生物学研究的首要对象,系统发育重建和个体发育剖析的结合将促进认知花的形态进化。发育相关基因的进化表现为等位基因遗传或表观遗传的突变,基因家族生与死的进化,不同基因组拥有独特的基因。运用形态学或序列分析方法很大程度揭示了禾本科植物花进化过程中的基因进化。试从学科问题、思路方法以及具体例子介绍植物进化发育生物学。     

Structure trees and species trees: what they say about morphological development and evolution

The evolutionary history of morphological structures generally is equated with that of the taxa that carry them. It is argued here that, analogous to genes, developmental genetic pathways underlying morphological structures may be subject to developmental evolutionary changes that result, for instance, in duplication (serial homology analogous to gene duplication and paralogy). Entities that undergo evolution are expected to be related to each other as a tree. Just as with molecular evolution, "structure trees" and species trees sometimes may be incongruent, with implications for morphological homology concepts. Detection of structure trees through morphological evolutionary analyses may point to an entity that is maintained through evolution, possibly in part because it is a developmentally integrated structure ("individualized"). This idea is illustrated in a morphological evolutionary analysis of leaf primordia. These analyses suggest that leaf primordia in monocots and close relatives are related to each other as a tree and, therefore, are developmentally integrated, evolving entities. Among monocot primordia this tree structure breaks down, and it is concluded that there is no entity, the "monocot leaf primordium." However, one group of primordia is identified within monocots that have uniform characteristics and that are well represented by model species maize and rice. Such analyses of structure trees can facilitate the extrapolation and interpretation of results from molecular developmental and other comparative studies.     

花、基因、禾本科

进化发育生物学的一个重要任务就是揭示形态多样性的分子基础, 该领域的研究包含形态、形态发育相关基因和形态所属类群等三个要素。花/花序是进化发育生物学研究的首要对象, 系统发育重建和个体发育剖析的结合将促进认知花的形态进化。发育相关基因的进化表现为等位基因遗传或表观遗传的突变, 基因家族生与死的进化, 不同基因组拥有独特的基因。运用形态学或序列分析方法很大程度揭示了禾本科植物花进化过程中的基因进化。试从学科问题、思路方法以及具体例子介绍植物进化发育生物学。     

Gene regulatory landscape of the sonic hedgehog locus in embryonic development

The organs of vertebrate species display a wide variety of morphology. A remaining challenge in evolutionary developmental biology is to elucidate how vertebrate lineages acquire distinct morphological features. Developmental programs are driven by spatiotemporal regulation of gene expression controlled by hundreds of thousands of cis-regulatory elements. Changes in the regulatory elements caused by the introduction of genetic variants can confer regulatory innovation that may underlie morphological novelties. Recent advances in sequencing technology have revealed a number of potential regulatory variants that can alter gene expression patterns. However, a limited number of studies demonstrate causal dependence between genetic and morphological changes. Regulation of Shh expression is a good model to understand how multiple regulatory elements organize tissue-specific gene expression patterns. This model also provides insights into how evolution of molecular traits, such as gene regulatory networks, lead to phenotypic novelty.     

EST and transcriptome analysis of cephalochordate amphioxus--past, present and future

The cephalochordates, commonly known as amphioxus or lancelets, are now considered the most basal chordate group, and the studies of these organisms therefore offer important insights into various levels of evolutionary biology. In the past two decades, the investigation of amphioxus developmental biology has provided key knowledge for understanding the basic patterning mechanisms of chordates. Comparative genome studies of vertebrates and amphioxus have uncovered clear evidence supporting the hypothesis of two-round whole-genome duplication thought to have occurred early in vertebrate evolution and have shed light on the evolution of morphological novelties in the complex vertebrate body plan. Complementary to the amphioxus genome-sequencing project, a large collection of expressed sequence tags (ESTs) has been generated for amphioxus in recent years; this valuable collection represents a rich resource for gene discovery, expression profiling and molecular developmental studies in the amphioxus model. Here, we review previous EST analyses and available cDNA resources in amphioxus and discuss their value for use in evolutionary and developmental studies. We also discuss the potential advantages of applying high-throughput, next-generation sequencing (NGS) technologies to the field of amphioxus research.     

Leaf surface development and the plant fossil record: stomatal patterning in Bennettitales

Stomata play a critical ecological role as an interface between the plant and its environment. Although the guard‐cell pair is highly conserved in land plants, the development and patterning of surrounding epidermal cells follow predictable pathways in different taxa that are increasingly well understood following recent advances in the developmental genetics of the plant epidermis in model taxa. Similarly, other aspects of leaf development and evolution are benefiting from a molecular–genetic approach. Applying this understanding to extinct taxa known only from fossils requires use of extensive comparative morphological data to infer ‘fossil fingerprints’ of developmental evolution (a ‘palaeo‐evo‐devo’ perspective). The seed‐plant order Bennettitales, which flourished through the Mesozoic but became extinct in the Late Cretaceous, displayed a consistent and highly unusual combination of epidermal traits, despite their diverse leaf morphology. Based on morphological evidence (including possession of flower‐like structures), bennettites are widely inferred to be closely related to angiosperms and hence inform our understanding of early angiosperm evolution. Fossil bennettites – even purely vegetative material – can be readily identified by a combination of epidermal features, including distinctive cuticular guard‐cell thickenings, lobed abaxial epidermal cells (‘puzzle cells’), transverse orientation of stomata perpendicular to the leaf axis, and a pair of lateral subsidiary cells adjacent to each guard‐cell pair (termed paracytic stomata). Here, we review these traits and compare them with analogous features in living taxa, aiming to identify homologous – and hence phylogenetically informative – character states and to increase understanding of developmental mechanisms in land plants. We propose a range of models addressing different aspects of the bennettite epidermis. The lobed abaxial epidermal cells indicate adaxial–abaxial leaf polarity and associated differentiated mesophyll that could have optimised photosynthesis. The typical transverse orientation of the stomata probably resulted from leaf expansion similar to that of a broad‐leaved monocot such as Lapageria, but radically different from that of broad‐leafed eudicots such as Arabidopsis. Finally, the developmental origin of the paired lateral subsidiary cells – whether they are mesogene cells derived from the same cell lineage as the guard‐mother cell, as in some eudicots, or perigene cells derived from an adjacent cell lineage, as in grasses – represents an unusually lineage‐specific and well‐characterised developmental trait. We identify a close similarity between the paracytic stomata of Bennettitales and the ‘living fossil’ Gnetum, strongly indicating that (as in Gnetum) the pair of lateral subsidiary cells of bennettites are both mesogene cells. Together, these features allow us to infer development in this diverse and relatively derived lineage that co‐existed with the earliest recognisable angiosperms, and suggest that the use of these characters in phylogeny reconstruction requires revision.     

Butterfly wing patterns

This paper integrates genetical studies of variation in the wing patterns of Lepidoptera with experimental investigations of developmental mechanisms. Research on the tropical butterfly,Bicyclus anynana, is described. This work includes artificial selection of lines with different patterns of wing eyespots followed by grafting experiments on the lines to examine the phenotypic and genetic differences in terms of developmental mechanisms. The results are used to show how constraints on the evolution of this wing pattern may be related to the developmental organisation. The eyespot pattrn can be envisaged as a set of developmental homologues; a common developmental mechanism is associated with a quantitative genetic system involving high genetic correlations. However, individual genes which influence only subsets of the eyespots, thus uncoupling the interdependence of the eyespots, may be important in evolutionary change. The postulated evolutionary constraints are illustrated with respect to differences in wing pattern found among other species ofBicyclus.     

Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution

Biologists have long sought to understand which genes and what kinds of changes in their sequences are responsible for the evolution of morphological diversity. Here, I outline eight principles derived from molecular and evolutionary developmental biology and review recent studies of species divergence that have led to a genetic theory of morphological evolution, which states that (1) form evolves largely by altering the expression of functionally conserved proteins, and (2) such changes largely occur through mutations in the cis-regulatory sequences of pleiotropic developmental regulatory loci and of the target genes within the vast networks they control.     

Vegetative morphology and anatomy of Maundia (Maundiaceae: Alismatales) and patterns of peripheral bundle orientation in angiosperm leaves with three‐dimensional venation

Collateral bundles with external position of the phloem characterize the stem vasculature of most seed plants. An earlier study highlighted the occurrence of inverted peripheral bundles in the leafless inflorescence peduncle of the rare Australian aquatic Maundia triglochinoides. This unusual feature and other morphological and molecular data supported the recognition of the monogeneric Maundiaceae, but the anatomy of the leaves, rhizomes and roots of Maundia remained unknown and is studied here. Maundia has an iterative sympodial growth with all shoots bearing five tubular cataphylls splitting longitudinally and simulating open sheaths at maturity and two (or three) linear foliage leaves without a conspicuous basal sheath. This morphology distinguishes Maundiaceae from all other Alismatales. The rhizome has an atactostele with collateral bundles of normal orientation; peripheral bundles are absent. Cataphylls have a series of normally oriented bundles. Foliage leaves are thick, bifacial, semi‐elliptical in cross‐section, with a thin subepidermal layer of chlorenchyma on both sides, accompanied by peripheral bundles with xylem facing outwards (thus abaxial peripheral bundles are inverted) and central large bundles of normal orientation. Strong anatomical similarity between leaves and peduncles is related to their shared function as assimilatory organs. As in angiosperm succulents, the three‐dimensional leaf venation in thick aquatic and helophyte leaves of Alismatales serves to reduce transport distances between veins and photosynthetic cells. In both cases, the patterns of orientation of peripheral bundles (with inverted adaxial or abaxial bundles) are unstable in large clades. These slender bundles cannot be used for the identification of unifacial leaves. Some anatomical characters express homoplastic similarities between Maundiaceae and Aponogetonaceae.     

Genetics, development and evolution of adaptive pigmentation in vertebrates

The study of pigmentation has played an important role in the intersection of evolution, genetics, and developmental biology. Pigmentation's utility as a visible phenotypic marker has resulted in over 100 years of intense study of coat color mutations in laboratory mice, thereby creating an impressive list of candidate genes and an understanding of the developmental mechanisms responsible for the phenotypic effects. Variation in color and pigment patterning has also served as the focus of many classic studies of naturally occurring phenotypic variation in a wide variety of vertebrates, providing some of the most compelling cases for parallel and convergent evolution. Thus, the pigmentation model system holds much promise for understanding the nature of adaptation by linking genetic changes to variation in fitness-related traits. Here, I first discuss the historical role of pigmentation in genetics, development and evolutionary biology. I then discuss recent empirically based studies in vertebrates, which rely on these historical foundations to make connections between genotype and phenotype for ecologically important pigmentation traits. These studies provide insight into the evolutionary process by uncovering the genetic basis of adaptive traits and addressing such long-standing questions in evolutionary biology as (1) are adaptive changes predominantly caused by mutations in regulatory regions or coding regions? (2) is adaptation driven by the fixation of dominant mutations? and (3) to what extent are parallel phenotypic changes caused by similar genetic changes? It is clear that coloration has much to teach us about the molecular basis of organismal diversity, adaptation and the evolutionary process.     

中国兽类遗传与进化研究进展与展望

中国兽类物种丰富,且具有150个特有种。本文综述了60年来中国兽类遗传与进化的研究进展,内容涵盖系统发育关系重建、遗传多样性评估、种群遗传结构、适应性进化以及趋同进化的分子机制。本文重点概述了食肉目（大、小熊猫）、有蹄类、翼手目、灵长目、小型兽类以及海兽类等重要类群的研究进展,为中国兽类的物种保护提供了重要资料。另外,本文还对中国兽类遗传与进化研究未来的研究方向提出几点建议,包括运用各种组学技术、筛选新型遗传标记和候选基因（调控序列）、结合表观遗传学并借助进化发育生物学研究方法,以期全面深入地理解中国兽类分类地位、起源以及特异表型产生和独特适应的发育遗传学机制等,进而实现“天人合一”保护生物学的新理念和新愿景。     

Comparative Genomics and Evolution of Avian Specialized Traits

Genomic data are important for understanding the origin and evolution of traits. Under the context of rapidly developing of sequencing technologies and more widely available genome sequences, researchers are able to study evolutionary mechanisms of traits via comparative genomic methods. Compared with other vertebrates, bird genomes are relatively small and exhibit conserved synteny with few repetitive elements, which makes them suitable for evolutionary studies. Increasing genomic progress has been reported on the evolution of powered flight, body size variation, beak morphology, plumage colouration, high-elevation colonization, migration, and vocalization. By summarizing previous studies, we demonstrate the genetic bases of trait evolution, highlighting the roles of small-scale sequence variation, genomic structural variation, and changes in gene interaction networks. We suggest that future studies should focus on improving the quality of reference genomes, exploring the evolution of regulatory elements and networks, and combining genomic data with morphological, ecological, behavioural, and developmental biology data.     

Evolution and development — the nematode vulva as a case study

To understand how morphological characters change during evolution, we need insight into the evolution of developmental processes. Comparative developmental approaches that make use of our fundamental understanding of development in certain model organisms have been initiated for different animal systems and flowering plants. Nematodes provide a useful experimental system with which to investigate the genetic and molecular alterations underlying evolutionary changes of cell fate specification in development, by comparing different species to the genetic model system Caenorhabditis elegans. In this review, I will first discuss the different types of evolutionary alterations seen at the cellular level by focusing mainly on the analysis of vulva development in different species. The observed alterations involve changes in cell lineage, cell migration and cell death, as well as induction and cell competence. I then describe a genetic approach in the nematode Pristionchus pacificus that might identify those genetic and molecular processes that cause evolutionary changes of cell fate specification.