Assessing the phylogenetic utility of sequence heterochrony: evolution of avian ossification sequences as a case study

The evolution of developmental sequences, or sequence heterochrony, is an emerging field of study that addresses the temporal interplay between evolution and development. Some phylogenetic signal has been found in developmental sequence data, but sampling has generally been limited to small numbers of taxa and few developmental events. Here we present the largest ossification sequence dataset to date. The sequences are composed of ossification events throughout the avian skeleton, and are used to address the evolutionary signal of ossification sequence data within this clade. The results indicate that ossification sequences are conserved in birds, and show a stronger phylogenetic signal than previous studies, perhaps due to the volume of data. Phylogenetic signal is not strong enough, however, to consider ossification sequence data to be any better at resolving phylogenetic hypotheses than other morphological data and just as prone to evolutionary convergence. There is no one-to-one correlation between ossification sequence and developmental stage. We discuss some methodological implications of our findings, as well as commonalities in avian ossification sequences such as early ossification of the long bones relative to the dermatocranium, and of the hindlimb over the forelimb.     

Cranial modularity and sequence heterochrony in mammals

Heterochrony, the temporal shifting of developmental events relative to each other, requires a degree of autonomy among those processes or structures. Modularity, the division of larger structures or processes into autonomous sets of internally integrated units, is often discussed in relation to the concept of heterochrony. However, the relationship between the developmental modules derived from studies of heterochrony and evolutionary modules, which should be of adaptive importance and relate to the genotype-phenotype map, has not been explicitly studied. I analyzed a series of sectioned and whole cleared-and-stained embryological and neonatal specimens, supplemented with published ontogenetic data, to test the hypothesis that bones within the same phenotypic modules, as determined by morphometric analysis, are developmentally integrated and will display coordinated heterochronic shifts across taxa. Modularity was analyzed in cranial bone ossification sequences of 12 therian mammals. A dataset of 12-18 developmental events was used to assess if modularity in developmental sequences corresponds to six phenotypic modules, derived from a recent morphometric analysis of cranial modularity in mammals. Kendall's tau was used to measure rank correlations, with randomization tests for significance. If modularity in developmental sequences corresponds to observed phenotypic modules, bones within a single phenotypic module should show integration of developmental timing, maintaining the same timing of ossification relative to each other, despite differences in overall ossification sequences across taxa. Analyses did not find any significant conservation of developmental timing within the six phenotypic modules, meaning that bones that are highly integrated in adult morphology are not significantly integrated in developmental timing.     

Estimating evolution of temporal sequence changes: a practical approach to inferring ancestral developmental sequences and sequence heterochrony

Developmental biology often yields data in a temporal context. Temporal data in phylogenetic systematics has important uses in the field of evolutionary developmental biology and, in general, comparative biology. The evolution of temporal sequences, specifically developmental sequences, has proven difficult to examine due to the highly variable temporal progression of development. Issues concerning the analysis of temporal sequences and problems with current methods of analysis are discussed. We present here an algorithm to infer ancestral temporal sequences, quantify sequence heterochronies, and estimate pseudoreplicate consensus support for sequence changes using Parsimov-based genetic inference [PGi]. Real temporal developmental sequence data sets are used to compare PGi with currently used approaches, and PGi is shown to be the most efficient, accurate, and practical method to examine biological data and infer ancestral states on a phylogeny. The method is also expandable to address further issues in developmental evolution, namely modularity.     

Sequence heterochrony and the evolution of development

One of the most persistent questions in comparative developmental biology concerns whether there are general rules by which ontogeny and phylogeny are related. Answering this question requires conceptual and analytic approaches that allow biologists to examine a wide range of developmental events in well-structured phylogenetic contexts. For evolutionary biologists, one of the most dominant approaches to comparative developmental biology has centered around the concept of heterochrony. However, in recent years the focus of studies of heterochrony largely has been limited to one aspect, changes in size and shape. I argue that this focus has restricted the kinds of questions that have been asked about the patterns of developmental change in phylogeny, which has narrowed our ability to address some of the most fundamental questions about development and evolution. Here I contrast the approaches of growth heterochrony with a broader view of heterochrony that concentrates on changes in developmental sequence. I discuss a general approach to sequence heterochrony and summarize newly emerging methods to analyze a variety of kinds of developmental change in explicit phylogenetic contexts. Finally, I summarize a series of studies on the evolution of development in mammals that use these new approaches.     

A new technique for identifying sequence heterochrony

Sequence heterochrony (changes in the order in which events occur) is a potentially important, but relatively poorly explored, mechanism for the evolution of development. In part, this is because of the inherent difficulties in inferring sequence heterochrony across species. The event-pairing method, developed independently by several workers in the mid-1990s, encodes sequences in a way that allows them to be examined in a phylogenetic framework, but the results can be difficult to interpret in terms of actual heterochronic changes. Here, we describe a new, parsimony-based method to interpret such results. For each branch of the tree, it identifies the least number of event movements (heterochronies) that will explain all the observed event-pair changes. It has the potential to find all alternative, equally parsimonious explanations, and generate a consensus, containing the movements that form part of every equally most parsimonious explanation. This new technique, which we call Parsimov, greatly increases the utility of the event-pair method for inferring instances of sequence heterochrony.     

A large‐scale survey of heterochrony in anuran cranial ossification patterns

Most anurans have a biphasic life cycle, which includes metamorphosis from a tadpole stage to an adult frog. This process involves extensive transformations of the cranial skeleton, which have been of long‐standing interest with respect to anuran skeletal evolution and taxonomy. In this study, large‐scale patterns of anuran skeletal ossification are assessed by collecting the most comprehensive data set on anuran cranial ossification to date from the literature, including data for 45 anuran and one caudate outgroup species. Ossification sequences were translated into event‐pair matrices for explorative phylogenetic analysis and phylogenetically informed parsimony search for heterochrony using the Parsimov algorithm. Rank variability of single bones across species was also analysed. Little phylogenetic signal was retrieved from a parsimony‐based phylogenetic analysis of event‐pairs, and only a few species that are generally agreed to be closely related are placed close to each other (e.g. some Pipidae and Costata). Parsimov analysis revealed some clade‐specific heterochrony in anuran clades of varying inclusiveness. Our results show that relating heterochronic changes in anuran cranial ontogeny to parameters such as direct development or miniaturization is problematic because of the high evolvability of cranial ossification sequences. Rank variation analysis suggests that anuran cranial bones are highly variable in their sequence positioning, possibly because tadpole and adult cranial morphology do not co‐evolve. Elements which are lost in some species ossify at the end of the sequence, providing evidence for the notion that failure of anuran cranial elements to ossify is due to processes of paedomorphosis.     

Time's arrow: heterochrony and the evolution of development

The concept of heterochrony, which denotes a change in the relative timing of developmental events and processes in evolution, has accompanied attempts to link evolution and development for well over a century. During this time the definition of heterochrony and the application of the concept have varied and by the late 1990's, many questioned the usefulness of the concept. However, in the past decade studies of heterochrony have been revitalized by a new focus on developmental sequence, an examination of heterochrony in explicit phylogenetic contexts and increasing tendencies to examine the heterochrony of many kinds of events, including cellular, molecular and genetic events. Examples of such studies are reviewed in this paper and it is argued that this new application of heterochrony provides an extraordinarily rich opportunity for understanding the developmental basis of evolutionary change.     

Modularity and heterochrony in the evolution of the ceratopsian dinosaur frill

The fossil record provides compelling examples of heterochrony at macroevolutionary scales such as the peramorphic giant antlers of the Irish elk. Heterochrony has also been invoked in the evolution of the distinctive cranial frill of ceratopsian dinosaurs such as Triceratops. Although ceratopsian frills vary in size, shape, and ornamentation, quantitative analyses that would allow for testing hypotheses of heterochrony are lacking. Here, we use geometric morphometrics to examine frill shape variation across ceratopsian diversity and within four species preserving growth series. We then test whether the frill constitutes an evolvable module both across and within species, and compare growth trajectories of taxa with ontogenetic growth series to identify heterochronic processes. Evolution of the ceratopsian frill consisted primarily of progressive expansion of its caudal and caudolateral margins, with morphospace occupation following taxonomic groups. Although taphonomic distortion represents a complicating factor, our data support modularity both across and within species. Peramorphosis played an important role in frill evolution, with acceleration operating early in neoceratopsian evolution followed by progenesis in later diverging cornosaurian ceratopsians. Peramorphic evolution of the ceratopsian frill may have been facilitated by the decoupling of this structure from the jaw musculature, an inference that predicts an expansion of morphospace occupation and higher evolutionary rates among ceratopsids as indeed borne out by our data. However, denser sampling of the meager record of early‐diverging taxa is required to test this further.     

Paedomorphosis and heterochrony in the origin and evolution of the class holothuroidea

The role of paedomorphosis as a particular case of heterochrony in the origin and evolution of the class Holothuroidea is analyzed. It is shown that holothurians are characterized by the presence of some paedomorphic characters (reduced skeleton, absence of an axial complex in the shape of a morphologically integrated structure, single gonad with one gonopore). In many members of the subclass Holothuriacea, sclerites of the body wall are arranged in two layers. Sclerites of the deeper layer develop as a perforated plate and correspond to the skeletal elements forming in other echinoderms the body skeleton, for example, the test of sea urchins. Sclerites of the superficial layer frequently look like various tables, develop like spines of other echinoderm classes, in particular, juvenile tetraradiate spines of sea urchins, and correspond to spines of other classes of Echinodermata. Ontogenetic changes at the stage of five first tentacles resulted in interruption at an early stage of the development with the catastrophic metamorphosis, which is typical for other Eleutherozoa. The ontogeny of holothurians acquired the evolutive (gradual) character; the adult body began to develop on the basis of the larval body and larval tissues were partially included in the body of adult holothurians. As a result, the place and developmental pattern of the radial complex of organs changed and heterochrony in the development of characters concerned with different coordination chains intensified; therefore, the modern body plan of holothurians was formed. The processes of paedomorphosis and heterochrony played an important role not only in the origin and formation of the class Holothuroidea, but also during its evolution. Paedomorphic processes became rather important in the evolution of the order Synaptida. Paedomorphic features are particularly prominent in the structure of small interstitial forms. In some holothurians, the paedomorphosis resulted in the change in relationships between symmetry planes. The bilateral plane of symmetry of these holothurians coincide with the plane of symmetry 2–1–2, which is positioned in the majority of holothurians at about 72° to the bilateral plane. Independently, but frequently in parallel, the intestinal loop disappeared, so that the gut became straight and suspended on mediodorsal mesentery almost throughout its extent. The combination of these processes in holothurians of the order Synaptida resulted in the formation of almost complete pentaradially bilateral symmetry.     

Evidence for heterochrony in the cranial evolution of fossil crocodyliforms

The southern supercontinent of Gondwana was home to an extraordinary diversity of stem‐crocodylians (Crocodyliformes) during the Late Cretaceous. The remarkable morphological disparity of notosuchian crocodyliforms indicates that this group filled a wide range of ecological roles more frequently occupied by other vertebrates. Among notosuchians, the distinctive cranial morphology and large body sizes of Baurusuchidae suggest a role as apex predators in ecosystems in which the otherwise dominant predatory theropod dinosaurs were scarce. Large‐bodied crocodyliforms, modern and extinct, are known to have reached large sizes by extending their growth period. In a similar way, peramorphic heterochronic processes may have driven the evolution of the similarly large baurusuchids. To assess the presence of peramorphic processes in the cranial evolution of baurusuchids, we applied a geometric morphometric approach to investigate ontogenetic cranial shape variation in a comprehensive sample of notosuchians. Our results provide quantitative morphological evidence that peramorphic processes influenced the cranial evolution of baurusuchids. After applying size and ancestral ontogenetic allometry corrections to our data, we found no support for the action of either hypermorphosis or acceleration, indicating that these two processes alone cannot explain the shape variation observed in Notosuchia. Nevertheless, the strong link between cranial shape variation and size increase in baurusuchids suggests that peramorphic processes were involved in the emergence of hypercarnivory in these animals. Our findings illustrate the role of heterochrony as a macroevolutionary driver, and stress, once more, the usefulness of geometric morphometric techniques for identifying heterochronic processes behind evolutionary trends.     

The dentary of hadrosauroid dinosaurs: evolution through heterochrony

The near-global distribution of hadrosaurid dinosaurs during the Cretaceous has been attributed to mastication, a behaviour commonly recognized as a mammalian adaptation. Its occurrence in a non-mammalian lineage should be accompanied by the evolution of several morphological modifications associated with food acquisition and processing. This study investigated morphological variation in the dentary, a major element of the hadrosauroid lower jaw. Eighty-four hadrosauroid dentaries were subjected to geometric morphometric and statistical analyses to investigate their taxonomic, ontogenetic, and individual variation. Results suggest increased food acquisition and processing efficiency in saurolophids through a complex pattern of evolutionary and growth-related changes. The edentulous region grew longer relative to dentary length, allowing for food acquisition specialization anteriorly and processing posteriorly, and became ventrally directed, possibly associated with foraging low-growing vegetation, especially in younger individuals. The saurolophid coronoid process became anteriorly directed and relatively more elongate, with an expanded apex, increasing moment arm length, with muscles pulling the jaw more posteriorly, increasing mechanical advantage. During growth, all hadrosauroids underwent anteroposterior dental battery elongation by the addition of teeth, and edentulous region ventralization decreased. The dental battery became deeper in saurolophids by increasing the number of teeth per tooth family. The increased coronoid process anterior inclination and relative edentulous region elongation in saurolophids are hypothesized to have evolved through hypermorphosis and/or acceleration, peramorphic heterochronic processes; the development of an anteroposteriorly shorter but dorsoventrally taller saurolophid dentary, is probably due to post-displacement in dental battery elongation and edentulous region decreased ventral orientation, a paedomorphic heterochronic process.     

Skeletogenesis and sequence heterochrony in rodent evolution, with particular emphasis on the African striped mouse, Rhabdomys pumilio (Mammalia)

Data documenting skeletal development in rodents, the most species-rich ‘order’ of mammals, are at present restricted to a few model species, a shortcoming that hinders exploration of the morphological and ecological diversification of the group. In this study we provide the most comprehensive sampling of rodent ossification sequences to date, with the aim of exploring whether heterochrony is ubiquitous in rodent evolution at the onset of skeletal formation. The onset of ossification in 17 cranial elements and 24 postcranial elements was examined for eight muroid and caviomorph rodent species. New data are provided for two non-model species. For one of these, the African striped mouse, Rhabdomys pumilio, sampling was extended by studying 53 autopodial elements and examining intraspecific variation. The Parsimov method of studying sequence heterochrony was used to explore the role that changes in developmental timing play in early skeletal formation. Few heterochronies were found to diagnose the muroid and caviomorph clades, suggesting conserved patterning in skeletal development. Mechanisms leading to the generation of the wide range of morphological diversity encapsulated within Rodentia may be restricted to later periods in development than those studied in this work. Documentation of skeletogenesis in Rhabdomys indicates that intraspecifc variation in ossification sequence pattern is present, though not extensive. Our study suggests that sequence heterochrony is neither pivotal nor prevalent during early skeletal formation in rodents.     

Skeletal heterochrony is associated with the anatomical specializations of snakes among squamate reptiles

Snakes possess a derived anatomy, characterized by limb reduction and reorganization of the skull and internal organs. To understand the origin of snakes from an ontogenetic point of view, we conducted comprehensive investigations on the timing of skeletal elements, based on published and new data, and reconstructed the evolution of the ossification sequence among squamates. We included for the first time Varanus, a critical taxon in phylogenetic context. There is comprehensive delay in the onset of ossification of most skeletal elements in snakes when compared to reference developmental events through evolution. We hypothesize that progressing deceleration accompanied limb reduction and reorganization of the snake skull. Molecular and morphological studies have suggested close relationship of snakes to either amphisbaenians, scincids, geckos, iguanids, or varanids. Likewise, alternative hypotheses on habitat for stem snakes have been postulated. Our comprehensive heterochrony analyses detected developmental shifts in ossification for each hypothesis of snake origin. Moreover, we show that reconstruction of ancestral developmental sequences is a valuable tool to understand ontogenetic mechanisms associated with major evolutionary changes and test homology hypotheses. The “supratemporal” of snakes could be homolog to squamosal of other squamates, which starts ossification early to become relatively large in snakes.     

Skeletal development in the African elephant and ossification timing in placental mammals

We provide here unique data on elephant skeletal ontogeny. We focus on the sequence of cranial and post-cranial ossification events during growth in the African elephant (Loxodonta africana). Previous analyses on ossification sequences in mammals have focused on monotremes, marsupials, boreoeutherian and xenarthran placentals. Here, we add data on ossification sequences in an afrotherian. We use two different methods to quantify sequence heterochrony: the sequence method and event-paring/Parsimov. Compared with other placentals, elephants show late ossifications of the basicranium, manual and pedal phalanges, and early ossifications of the ischium and metacarpals. Moreover, ossification in elephants starts very early and progresses rapidly. Specifically, the elephant exhibits the same percentage of bones showing an ossification centre at the end of the first third of its gestation period as the mouse and hamster have close to birth. Elephants show a number of features of their ossification patterns that differ from those of other placental mammals. The pattern of the initiation of the ossification evident in the African elephant underscores a possible correlation between the timing of ossification onset and gestation time throughout mammals.     

Comparative anatomy and histology of xenarthran osteoderms

Reconstruction of soft tissues in fossil vertebrates is an enduring challenge for paleontologists. Because inferences must be based on evidence from hard tissues (typically bones or teeth), even the most complete fossils provide only limited information about certain organ systems. Osteoderms ("dermal armor") are integumentary bones with high fossilization potential that hold information about the anatomy of the skin in many extant and fossil amniotes. Their importance for functional morphology and phylogenetic research has recently been recognized, but studies have focused largely upon reptiles, in which osteoderms are most common. Among mammals, osteoderms occur only in members of the clade Xenarthra, which includes armadillos and their extinct relatives: glyptodonts, pampatheres, and, more distantly, ground sloths. Here, I present new information on the comparative morphology and histology of osteoderms and their associated soft tissues in 11 extant and fossil xenarthrans. Extinct mylodontid sloths possessed simple, isolated ossicles, the presence of which is likely plesiomorphic for Xenarthra. More highly derived osteoderms of glyptodonts, pampatheres, and armadillos feature complex articulations and surface ornamentation. Osteoderms of modern armadillos are physically associated with a variety of soft tissues, including nerve, muscle, gland, and connective tissue. In some cases, similar osteological features may be caused by two or more different tissue types, rendering soft-tissue inferences for fossil osteoderms equivocal. Certain osteological structures, however, are consistently associated with specific soft-tissue complexes and therefore represent a relatively robust foundation upon which to base soft-tissue reconstructions of extinct xenarthrans.     

Nonheterochronic developmental changes underlie morphological heterochrony in the evolution of the Ardeidae

Evolutionary changes in developmental timing and rates (heterochrony) are a source of morphological variation. Here we explore a central issue in heterochronic analysis: are the alterations in developmental timing and rates the only factor underlying morphological heterochrony? Tarsometatarsal growth through endochondral ossification in Ardeidae evolution has been taken as a case study. Evolutionary changes in bone growth rate (morphological heterochrony) might be either (a) the result of alterations in the mitotic frequency of epiphyseal chondrocytes (process‐heterochrony hypothesis), or (b) the outcome of alterations in the number of proliferating cells or in the size of hypertrophic chondrocytes (structural hypothesis). No correlation was found between tarsometatarsal growth rates and the frequency of cell division. However, bone growth rates were significantly correlated with the number of proliferating cells. These results support the structural hypothesis: morphological acceleration and deceleration are the outcome of evolutionary changes in one structural variable, the number of proliferating cells.