Reduce, reuse, and recycle: developmental evolution of trait diversification

A major focus of evolutionary developmental (evo-devo) studies is to determine the genetic basis of variation in organismal form and function, both of which are fundamental to biological diversification. Pioneering work on metazoan and flowering plant systems has revealed conserved sets of genes that underlie the bauplan of organisms derived from a common ancestor. However, the extent to which variation in the developmental genetic toolkit mirrors variation at the phenotypic level is an active area of research. Here we explore evidence from the angiosperm evo-devo literature supporting the frugal use of genes and genetic pathways in the evolution of developmental patterning. In particular, these examples highlight the importance of genetic pleiotropy in different developmental modules, thus reducing the number of genes required in growth and development, and the reuse of particular genes in the parallel evolution of ecologically important traits.     

Heterochronic detection through a function for the ontogenetic variation of bone shape

Heterochrony, evolutionary modifications in the rates and/or the timing of development, is widely recognized as an important agent of evolutionary change. In this paper, we are concerned with the detection of this evolutionary mechanism through the analysis of long bone growth. For this, we provide a function sigma (t) for the ontogenetic variation of bone shape by taking the ratio of two Gompertz curves explaining, respectively, the relative contribution to long bone growth of (a) endochondral ossification and (b) periosteal ossification. The significance of the fitting of this function to empirical data was tested in Anas platyrhynchos (Anseriformes). In this function sigma (t), the time t(m) at which periosteal growth rate first equalizes endochondral growth rate was taken as the timing parameter to be compared between taxa. On the other hand, the maximum rate of ontogenetic change in bone shape (maximum slope, beta) from hatching to t(m) was taken as the rate parameter to be compared. Comparisons of these parameters between the plesiomorphic condition and the derived character state would provide evidence for hypomorphosis (earlier occurrence of t(m)), hyper-morphosis (delayed occurrence of t(m)), deceleration (smaller beta) or acceleration (higher beta).Regarding the phylogenetic context, the ancestral condition for the character of interest should be estimated to polarize the direction of the heterochronic change. We have quantified the influence of the phylogenetic history on the variation of adult bone shape in a sample of 13 species of Anseriformes and 17 species from other neornithine orders of birds by using permutational phylogenetic regressions. Phylogenetic effects are significant, and this fact allows the optimization of bone shape onto a phylogenetic tree of Anseriformes to estimate the ancestral condition for Anas platyrhynchos.     

Human hyoid bones from the middle Pleistocene site of the Sima de los Huesos (Sierra de Atapuerca, Spain)

This study describes and compares two hyoid bones from the middle Pleistocene site of the Sima de los Huesos in the Sierra de Atapuerca (Spain). The Atapuerca SH hyoids are humanlike in both their morphology and dimensions, and they clearly differ from the hyoid bones of chimpanzees and Australopithecus afarensis. Their comparison with the Neandertal specimens Kebara 2 and SDR-034 makes it possible to begin to approach the question of temporal variation and sexual dimorphism in this bone in fossil humans. The results presented here show that the degree of metric and anatomical variation in the fossil sample was similar in magnitude and kind to living humans. Modern hyoid morphology was present by at least 530 kya and appears to represent a shared derived feature of the modern human and Neandertal evolutionary lineages inherited from their last common ancestor.     

Attachment structures in Rhizotrochus (Scleractinia): macro‐ to microscopic traits and their evolutionary significance

Marine sessile benthic organisms living on hard substrates have evolved a variety of attachment strategies. Rhizotrochus (Scleractinia, Flabellidae) is a representative azooxanthellate solitary scleractinian coral with a wide geographical distribution and unique attachment structures; it firmly attaches to hard substrates using numerous tube‐like rootlets, which are extended from a corallum wall, whereas most sessile corals are attached by stereome‐reinforced structures at their corallite bases. Detailed morphological and constructional traits of the rootlets themselves, along with their evolutionary significance, have not yet been fully resolved. Growth and developmental processes of spines in Truncatoflabellum and rootlets in Rhizotrochus suggest that these structures are homologous, as they both develop from the growth edges of walls and are formed by transformation of wall structures and their skeletal microstructures possess similar characteristics, such as patterns of rapid accretion and thickening deposits. Taking molecular phylogeny and fossil records of flabellids into consideration, Rhizotrochus evolved from a common free‐living ancestor and invaded hard‐substrate habitats by exploiting rootlets of spines origin, which were adaptive for soft‐substrate environments.     

The molecular signal for the adaptation to cold temperature during early life on Earth

Several lines of evidence such as the basal location of thermophilic lineages in large-scale phylogenetic trees and the ancestral sequence reconstruction of single enzymes or large protein concatenations support the conclusion that the ancestors of the bacterial and archaeal domains were thermophilic organisms which were adapted to hot environments during the early stages of the Earth. A parsimonious reasoning would therefore suggest that the last universal common ancestor (LUCA) was also thermophilic. Various authors have used branch-wise non-homogeneous evolutionary models that better capture the variation of molecular compositions among lineages to accurately reconstruct the ancestral G + C contents of ribosomal RNAs and the ancestral amino acid composition of highly conserved proteins. They confirmed the thermophilic nature of the ancestors of Bacteria and Archaea but concluded that LUCA, their last common ancestor, was a mesophilic organism having a moderate optimal growth temperature. In this letter, we investigate the unknown nature of the phylogenetic signal that informs ancestral sequence reconstruction to support this non-parsimonious scenario. We find that rate variation across sites of molecular sequences provides information at different time scales by recording the oldest adaptation to temperature in slow-evolving regions and subsequent adaptations in fast-evolving ones.     

Process heterochronies in endochondral ossification

Heterochrony, evolutionary changes in developmental rates and timing, is a key concept in the construction of a synthesis of development and evolution. Heterochronic changes in vertebrate evolution have traditionally been identified through plesiomorphic-apomorphic comparisons of bone growth. This methodological framework assumes that observed heterochronies are the outcome of dissociations of developmental processes in time. Recent findings of non-heterochronic developmental changes underlying morphological heterochrony invalidate this assumption. In this paper, a function for bone growth (at the organ level) has been mathematically deduced from the underlying developmental mechanisms. The temporal domain of the model spans from the time at maximum growth rate, after the formation of growth plates, to the time at atrophy of the proliferating stratum of cells. Three organizational levels were considered: (a) cell kinetics of endochondral ossification, (b) variation of bone growth rates and (c) variation of accumulated bone growth with increasing age. This quantitative model provides an excellent tool to deal with the problem of the developmental basis of morphological change. I have modelled potential evolutionary changes on the system at different levels of biological organization. This new framework involves an epistemological shift in heterochronic analysis from a pattern-oriented inductive way to a process-oriented deductive way. The analysis of the relationships between the evolutionary alterations of endochondral ossification and the morphological expression of these changes reveals that observed pattern heterochronies can be the outcome of different process heterochronies. Moreover, I discuss at length the heteroposic hypothesis, that evolutionary changes in the tight regulation of the amount of protein synthesized by a cell population during development would underlie acceleration or deceleration in cases of evolutionary changes in the initial number of proliferating cells at growth plates. Future research on the genetic basis of process heterochronies and heteroposies will complete our understanding of these evolutionary phenomena.     

Covariation of larval gene expression and adult body size in natural populations of Drosophila melanogaster

Understanding adaptive phenotypic variation is one of the most fundamental problems in evolutionary biology. Genes involved in adaptation are most likely those that affect traits most intimately connected to fitness: life-history traits. The genetics of quantitative trait variation (including life histories) is still poorly understood, but several studies suggest that (1) quantitative variation might be the result of variation in gene expression, rather than protein evolution, and (2) natural variation in gene expression underlies adaptation. The next step in studying the genetics of adaptive phenotypic variation is therefore an analysis of naturally occuring covariation of global gene expression and a life-history trait. Here, we report a microarray study addressing the covariation in larval gene expression and adult body weight, a life-history trait involved in adaptation. Natural populations of Drosophila melanogaster show adaptive geographic variation in adult body size, with larger animals at higher latitudes. Conditions during larval development also affect adult size with larger flies emerging at lower temperatures. We found statistically significant differences in normalized larval gene expression between geographic populations at one temperature (genetic variation) and within geographic populations between temperatures (developmental plasticity). Moreover, larval gene expression correlated highly with adult weight, explaining 81% of its natural variation. Of the genes that show a correlation of gene expression with adult weight, most are involved in cell growth or cell maintenance or are associated with growth pathways.     

Ontogeny and limb bone scaling in two new world marsupials,Monodelphis domestica and Didelphis virginiana

This study examines the growth of two species of marsupials who share common ancestry and are born at the same neonatal size of a little less than 1 g. Despite this similarity at birth, adult size of these two species differs by about 50 times, with the smaller species believed to be the more ancestral. We quantified the growth in the limb bones (humerus, femur, ulna, tibia, metacarpal, and metatarsal) beginning around 40 days of age until adult size was reached. Results indicate that the larger species grows at a higher rate of growth as well as for a longer period of time to reach its larger adult size. Despite these differences in growth, there were few differences observed in the scaling over time of length to width in the various limb bones that were measured. The two species, although different in their adult size and the patterns of growth, maintain the same length to width proportions in each limb bone. The biggest difference between species in scaling was observed in the bones of the hands and feet, which may suggest adaptation to size and/or locomotor performance as body size increases. Despite variation in size, these heterochronic patterns do not affect the shape among adults or over evolutionary time. J Morphol 231:117–130, 1997. © 1997 Wiley-Liss, Inc.     

Where to draw the nonprimate-primate taxonomic boundary.

The known Cretaceous and Paleocene primates, the Paromomyiformes, although lacking a fully developed postorbital bar, are nevertheless, both cladistically and phenetically, closest to the common ancestor of the living primates. Not only their undisputed phylogenetic ties but also their early experiments inthe arboreal milieu necessitate their balanced evolutionary classification within the order Primates.     

Developmental and genetic origins of murine long bone length variation

If we wish to understand whether development influences the rate or direction of morphological evolution, we must first understand the developmental bases of morphological variation within species. However, quantitative variation in adult morphology is the product of molecular and cellular processes unfolding from embryonic development through juvenile growth to maturity. The Atchley-Hall model provides a useful framework for dissecting complex morphologies into their component parts as a way of determining which developmental processes contribute to variation in adult form. We have examined differences in postnatal allometry and the patterns of genetic correlation between age-specific traits for ten recombinant inbred strains of mice generated from an intercross of LG/J and SM/J. Long bone length is closely tied to body size, but variation in adult morphology is more closely tied to differences in growth rate between 3 and 5 weeks of age. These analyses show that variation generated during early development is overridden by variation generated later in life. To more precisely determine the cellular processes generating this variation we then examined the cellular dynamics of long bone growth plates at the time of maximum elongation rate differences in the parent strains. Our analyses revealed that variation in long bone length is the result of faster elongation rates of the LG/J stain. The developmental bases for these differences in growth rate involve the rate of cell division and chondrocyte hypertrophy in the growth plate.     

The human extensor digitorum profundus muscle with comments on the evolution of the primate hand

Forelimb dissections on 14 genera of anthropoids including humans and 17 cases of human aneuploids has revealed a high incidence of “atavistic” musculature (Barash et al., 1970;Aziz, 1981a) in the aneuploids. The phenotypic specificity of this aneuploid musculature clearly manifests developmental retardation and instability (Shapiro, 1983) revealing not only the likely course of embryonic myogenesis in chromosomally normal humans (Cihak, 1972, 1977) but also information relevant to ontogenetic and evolutionary changes. The extensor digitorum profundus proprius complex is particularly illustrative of these characteristics of aneuploid musculature. Our examination of the variation of this muscle complex in human aneuploids and between primate genera reveals how normal ontogeny may proceed, as well as the morphological basis for the evolutionary changes in hand structure and function amongst Primates. We also consider the phylogenetic and functional significance of changes in the extensor digitorum profundus proprius with reference to the divergent locomotory and manipulative capabilities and behavior of Primates.     

Heterochrony: the Evolution of Development

Heterochrony can be defined as change to the timing or rate of development relative to the ancestor. Because organisms generally change in shape as well as increase in size during their development, any variation to the duration of growth or to the rate of growth of different parts of the organism can cause morphological changes in the descendant form. Heterochrony takes the form of both increased and decreased degrees of development, known as “peramorphosis” and “paedomorphosis,” respectively. These are the morphological consequences of the operation of processes that change the duration of the period of an individual’s growth, either starting or stopping it earlier or later than in the ancestor, or by extending or contracting the period of growth. Heterochrony operates both intra- and interspecifically and is the source of much intraspecific variation. It is often also the cause of sexual dimorphism. Selection of a sequence of species with a specific heterochronic trait can produce evolutionary trends in the form of pera- or paedomorphoclines. Many different life history traits arise from the operation of heterochronic processes, and these may sometimes be the targets of selection rather than morphological features themselves. It has been suggested that some significant steps in evolution, such as the evolution of vertebrates, were engendered by heterochrony. Human evolution was fuelled by heterochrony, with some traits, such as a large brain, being peramorphic, whereas others, such as reduced jaw size, are paedomorphic.     

Effect of photoperiod on development and growth in a pentatomid bug, Dolycoris baccarum

The effect of photoperiod on nymphal development, growth and adult size was examined in a pentatomid bug, Dolycoris baccarum , collected in Osaka (a warm temperate region) and Hokkaido (a subfrigid region), Japan. When insects were reared from eggs at 25°C, the developmental period was long and adult size was large under photoperiods close to the critical photoperiod for the induction of adult diapause. Adults of the Hokkaido population were larger than those of the Osaka population. There was no significant correlation between developmental period and adult size. Insects also showed variation in their growth rate: growth rate was low under photoperiods a little longer than the critical photoperiod for the induction of diapause. The ecological significance of variation in development and growth is discussed.     

There's something afoot in the evolution of ontogenies

Allometry, the association between size and shape, has long been considered an evolutionary constraint because of its ability to channel variation in particular directions in response to evolution of size. Several recent studies, however, have demonstrated that allometries themselves can evolve. Therefore, constraints based on these allometries are not constant over long evolutionary time scales. The changes in ontogeny appear to have a clear adaptive basis, which establishes a feedback loop from adaptive change of ontogeny through the altered developmental constraints to the potential for further evolutionary change. Altogether, therefore, this new evidence underscores the tight interactions between developmental and ecological factors in the evolution of morphological traits.     

Functional and ecological significance of rDNA intergenic spacer variation in a clonal organism under divergent selection for production rate

It has recently been hypothesized that variation in the intergenic spacer (IGS) of rDNA has considerable developmental, evolutionary and ecological significance through effects on growth rate and body C : N : P stoichiometry resulting from the role of the IGS in production of rRNA. To test these ideas, we assessed changes in size and structure of the repetitive region of the IGS, juvenile growth rate (JGR), RNA and phosphorus (P) contents in clonal lineages of Daphnia pulex derived from a single female and subjected to divergent selection on weight-specific fecundity (WSF). As a result of selection, WSF diverged rapidly, with significant reductions within two generations. Other significant changes accompanying shifts in WSF were that juveniles produced by low-WSF females grew more rapidly and had higher RNA and P contents. An increased predominance of long IGS variants was observed in lineages with elevated JGRs and low WSF. The observed variations in IGS length were related to the number of subrepeat units carrying a promoter sequence in the repetitive region. These results strongly support the hypothesized relationships, indicate a genetic mechanism for the evolution of such associations and demonstrate that Daphnia (and perhaps other parthenogens) possess considerable potential for rapid adaptive change in major life-history traits.     

Genetic and developmental basis for parallel evolution and its significance for hominoid evolution

Greater understanding of ape comparative anatomy and evolutionary history has brought a general appreciation that the hominoid radiation is characterized by substantial homoplasy.^1–4 However, little consensus has been reached regarding which features result from repeated evolution. This has important implications for reconstructing ancestral states throughout hominoid evolution, including the nature of the Pan‐Homo last common ancestor (LCA). Advances from evolutionary developmental biology (evo‐devo) have expanded the diversity of model organisms available for uncovering the morphogenetic mechanisms underlying instances of repeated phenotypic change. Of particular relevance to hominoids are data from adaptive radiations of birds, fish, and even flies demonstrating that parallel phenotypic changes often use similar genetic and developmental mechanisms. The frequent reuse of a limited set of genes and pathways underlying phenotypic homoplasy suggests that the conserved nature of the genetic and developmental architecture of animals can influence evolutionary outcomes. Such biases are particularly likely to be shared by closely related taxa that reside in similar ecological niches and face common selective pressures. Consideration of these developmental and ecological factors provides a strong theoretical justification for the substantial homoplasy observed in the evolution of complex characters and the remarkable parallel similarities that can occur in closely related taxa. Thus, as in other branches of the hominoid radiation, repeated phenotypic evolution within African apes is also a distinct possibility. If so, the availability of complete genomes for each of the hominoid genera makes them another model to explore the genetic basis of repeated evolution.     

Evaluating the role and measures of juvenile growth rate: latitudinal variation in insect life histories

Latitudinal and elevational trends in body size are found in numerous animal taxa, with various adaptive explanations proposed. It is however debatable whether geographic trends in adult body size are accompanied by corresponding differences in juvenile growth rate (= mass gain per unit time). Respective studies have been complicated by conceptual and methodological problems related to defining and measuring this variable, particularly in organisms with discontinuous growth like arthropods. Using an original method for estimating differential (instantaneous) juvenile growth rates, we compared geographically distant European populations of six insect species in a common garden experiment. We found no among population differences in differential growth rate in any of the species. This result is in concert with concurrent increase in both adult size and developmental time towards the south. While opposite examples exist, we interpret our results as challenging the view that growth rate is a trait that readily responds to environmentally based selective pressures. Our results thus advocate the more classical view of growth rate maximisation within its physiological limits. We discuss the advantages of using differential (rather than integral) measures of growth rate in evolutionary ecological studies and evaluate the reasons for the detected latitudinal trends in life history traits.     

Developmental basis of limb length in rodents: evidence for multiple divisions of labor in mechanisms of endochondral bone growth

SUMMARY Mammals are remarkably diverse in limb lengths and proportions, but the number and kind of developmental mechanisms that contribute to length differences between limb bones remain largely unknown. Intra- and interspecific differences in bone length could result from variations in the cellular processes of endochondral bone growth, creating differences in rates of chondrocyte proliferation or hypertrophy, variation in the shape and size of chondrocytes, differences in the number of chondrocytes in precursor populations and throughout growth, or a combination of these mechanisms. To address these questions, this study compared cellular mechanisms of endochondral bone growth in cross-sectional ontogenetic series of the appendicular skeleton of two rodent species: the mouse ( Mus musculus ) and Mongolian gerbil ( Meriones unguiculatus ). Results indicate that multiple cellular processes of endochondral bone growth contribute to phenotypic differences in limb bone length. The data also suggest that separate developmental processes contribute to intraspecific length differences in proximal versus distal limb bones, and that these proximo-distal mechanisms are distinct from mechanisms that contribute to interspecific differences in limb bone length related to body size. These developmental "divisions of labor" are hypothesized to be important features of vertebrate limb development that allow (1) morphology in the autopods to evolve independently of the proximal limb skeleton, and (2) adaptive changes in limb proportions related to locomotion to evolve independently of evolutionary changes in body size.     

Conservation and co-option in developmental programmes: the importance of homology relationships

One of the surprising insights gained from research in evolutionary developmental biology (evo-devo) is that increasing diversity in body plans and morphology in organisms across animal phyla are not reflected in similarly dramatic changes at the level of gene composition of their genomes. For instance, simplicity at the tissue level of organization often contrasts with a high degree of genetic complexity. Also intriguing is the observation that the coding regions of several genes of invertebrates show high sequence similarity to those in humans. This lack of change (conservation) indicates that evolutionary novelties may arise more frequently through combinatorial processes, such as changes in gene regulation and the recruitment of novel genes into existing regulatory gene networks (co-option), and less often through adaptive evolutionary processes in the coding portions of a gene. As a consequence, it is of great interest to examine whether the widespread conservation of the genetic machinery implies the same developmental function in a last common ancestor, or whether homologous genes acquired new developmental roles in structures of independent phylogenetic origin. To distinguish between these two possibilities one must refer to current concepts of phylogeny reconstruction and carefully investigate homology relationships. Particularly problematic in terms of homology decisions is the use of gene expression patterns of a given structure. In the future, research on more organisms other than the typical model systems will be required since these can provide insights that are not easily obtained from comparisons among only a few distantly related model species.     

Reiterative growth in the complex adaptive architecture of the Paleozoic (Pennsylvanian) filicalean fern Kaplanopteris clavata

Reiteration is a widespread component of plant growth whose evolutionary importance in ferns is not recognized widely. We introduce and discuss the growth architecture of Kaplanopteris clavata, a fossil filicalean fern from the Pennsylvanian (ca. 305 million yeas old), focusing on types of reiteration exhibited by this species and on the adaptive and phylogenetic significance of reiteration for ferns in general. Kaplanopteris clavata combines two types of reiterative growth where growth modules are borne on fronds: (1) entire fronds derived from primary pinnae, and (2) epiphyllous plantlets. This combination of reiterative pathways, unique among fossil and living ferns, allowed K. clavata to explore ecospace through an opportunistic combination of scrambling, climbing and epiphytic growth. Kaplanopteris clavata underscores the organographic importance of fronds (as opposed to stems) in the adaptive architecture of ferns, emphasizing functional convergences between the different Baupla̋ne of ferns and angiosperms. This unique combination of reiterative pathways is interpreted as a derived condition illustrating the structural and developmental complexity achieved by some filicaleans during the first major evolutionary radiation of leptosporangiate ferns.