Jo Wolfe

The study of ontogeny as an integral part of understanding the pattern of evolution dates back over 200 years, but only recently have ontogenetic data been explicitly incorporated into phylogenetic analyses. Pancrustaceans undergo radical ontogenetic changes. The spectacular upper Cambrian ‘Orsten’ fauna preserves phosphatized fossil larvae, including putative crown-group pancrustaceans with amazingly complete developmental sequences. The putative presence and nature of adult stages remains a source of debate, causing spurious placements in a traditional morphological analysis. We introduce a new coding method where each semaphoront (discrete larval or adult stage) is considered an OTU. This avoids a priori assumptions of heterochrony. Characters and their states are defined to identify changes in morphology throughout ontogeny. Phylogenetic analyses of semaphoronts produced relationships of each Orsten fossil to the crown-group clade expected from morphology shared with extant larvae. Bredocaris is a member of the stem lineage of Thecostraca or (Thecostraca + Copepoda), and Yicaris and Rehbachiella are likely members of the stem lineage of Cephalocarida. These placements rely directly on comparisons between extant and fossil larval character states. The position of Phosphatocopina remains unresolved. This method may have broader applications to other phylogenetic problems which may rely on ontogenetically variable homology statements.

The phenotype represents a critical interface between the genome and the envi-ronment in which organisms live and evolve. Phenotypic characters also are a rich source of biodiversity data for tree-building, and they enable scientists to reconstruct the evolu-tionary history of organisms, including most fossil taxa, for which genetic data are unavail-able. Therefore, phenotypic data are necessary for building a comprehensive Tree of Life. In contrast to recent advances in molecular sequencing, which has become faster and cheaper through recent technological advances, phenotypic data collection remains often prohibi-tively slow and expensive. The next-generation phenomics project is a collaborative, multidisciplinary effort to leverage advances in image analysis, crowdsourcing, and natural language processing to develop and implement novel approaches for discovering and scor-ing the phenome, the collection of phentotypic characters for a species. This research rep-resents a new approach to data collection that has the potential to transform phylogenetics research and to enable rapid advances in constructing the Tree of Life. Our goal is to as-semble large phenomic datasets built using new methods and to provide the public and sci-entific community with tools for phenomic data assembly that will enable rapid and auto-mated study of phenotypes across the Tree of Life.

This article provides a brief overview of the record of development in fossils, as well as a summary of the field of evo-devo, and uses examples from the scientific literature to illustrate some of the more abstract aspects of this principle. The contents are aimed at a non-specialist audience.

An ambitious, yet fundamental goal for comparative biology is to understand the evolutionary relationships for all of life. Yet many important taxonomic groups have remained recalcitrant to inclusion into broader scale studies. Here, we focus on collection of 9 new 454 transcriptome data sets from Ostracoda, an ancient and diverse group with a dense fossil record, which is often under-sampled in broader studies. We combine the new transcriptomes with a new morphological matrix (including fossils) and existing Expressed Sequence Tag (EST), mitochondrial genome, nuclear genome and rDNA data. Our analyses lead to new insights into ostracod and pancrustacean phylogeny. We obtained support for three epic pancrustacean clades that likely originated in the Cambrian: Oligostraca (Ostracoda, Mystacocarida, Branchiura, Pentastomida); Multicrustacea (Copepoda, Malacostraca, Thecostraca); and a clade we refer to as Allotriocarida (Hexapoda, Remipedia, Cephalocarida, Branchiopoda). Within the Oligostraca clade, our results support the unresolved question of ostracod monophyly. Within Multicrustacea, we find support for Thecostraca plus Copepoda, for which we suggest the name Hexanauplia. Within Allotriocarida, some analyses support the hypothesis that Remipedia is the sister taxon to Hexapoda, but others support Branchiopoda+Cephalocarida as the sister group of hexapods. In multiple different analyses, we see better support for equivocal nodes using slow-evolving genes or when excluding distant outgroups, highlighting the increased importance of conditional data combination in this age of abundant, often anonymous data. Yet, when we analyze the same set of species and ignore rate of gene evolution, we find higher support when including all data, more in line with a ‘total evidence’ philosophy. By concatenating molecular and morphological data, we place pancrustacean fossils in the phylogeny, which can be used for studies of divergence times in Pancrustacea, Arthropoda, or Metazoa. Our results and new data will allow for attributes of Ostracoda, such as its amazing fossil record and diverse biology, to be leveraged in broader scale comparative studies. Further, we illustrate how adding extensive next-generation sequence data from understudied groups can yield important new phylogenetic insights into long-standing questions, especially when carefully analyzed in combination with other data.

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Liu et al.1 described an 'armoured' lobopodian, Diania cactiformis, from the Chengjiang Lagerstätte (China; Cambrian, stage 3); this fossil bears potentially arthropod-like articulated and possibly sclerotized appendages, but lacks a sclerotized body. A cladistic analysis resolved Diania as sister-taxon to arthropods. From this phylogenetic position the authors tentatively inferred that arthropodization (sclerotization of limbs) may have preceded arthrodization (sclerotization of body elements) in arthropod evolution. Although we concur with the reasoning behind this inference, it rests on a phylogenetic placement that our analysis of the published data set does not reproduce."

The viviparous cockroach, Diploptera punctata, has been a valuable model organism for studies of the regulation of reproduction by juvenile hormone (JH) in insects. As a result of its truly viviparous mode of reproduction, precise regulation of JH biosynthesis and reproduction is required for production of offspring, providing a model system for the study of the relationship between JH production and oocyte growth and maturation. Most studies to date have focused on individuals isolated from a Hawaiian population of this species. A new population of this cockroach was found in Nakorn Pathom, Thailand, which demonstrated striking differences in cuticle pigmentation and mating behaviours, suggesting possible physiological differences between the two populations. To better characterize these differences, rates of JH release and oocyte growth were measured during the first gonadotrophic cycle. The Thai population was found to show significantly earlier increases in the rate of JH release, and oocyte development as compared with the Hawaiian population. Breeding experiments to determine the degree of interfertility between the two populations demonstrated greatly reduced fertility in crosses between the two populations. Additionally, levels of genetic divergence between the two populations estimated by sequencing a fragment of the mitochondrial 16S rRNA gene were surprisingly high. The significant differences in physiology and mating behaviours, combined with the reduced interfertility and high levels of sequence divergence, suggest that these two populations of D. punctata are quite distinct, and may even be in the process of speciation. Moreover, these studies have important implications for the study of JH function in the reproductive cycle of insects, as differences in timing of rates of JH biosynthesis may suggest a process of heterochrony in reproduction between the two populations.

The study of ontogeny as an integral part of understanding the pattern of evolution dates back over 200 years, but only recently have ontogenetic data been explicitly incorporated into phylogenetic analyses. Many (pan)crustaceans undergo radical ontogenetic changes. The spectacular upper Cambrian ‘Orsten’ fauna preserves phosphatized fossil larvae, including putative crown-group pancrustaceans with amazingly complete developmental sequences. The putative presence and nature of adult stages remains a source of debate, causing spurious placements in a traditional morphological analysis. I introduce a new coding method where each semaphoront (discrete larval or adult stage) is considered an OTU, avoiding a priori assumptions of heterochrony. Characters and their states are defined to identify changes in morphology throughout ontogeny. Phylogenetic analyses of semaphoronts produced relationships of each Orsten fossil on the stem lineages of clades expected from morphology shared with extant larvae (Thecostraca and Cephalocarida). These placements rely directly on comparisons between extant and fossil larval character states, and are of crucial importance in reconstructing paraphyletic Pancrustacea with morphological data (as well as polarizing character change). Current work extends this approach to phylogenomics, by sequencing transcriptomes of multiple semaphoronts of Decapoda. These methods may have broader applications to other phylogenetic problems which may rely on ontogenetically variable homology statements.

Pancrustaceans (= crustaceans + hexapods) undergo some of the most radical ontogenetic changes seen in the Metazoa. The spectacular upper Cambrian ‘Orsten’-type faunas preserve phosphatized fossil larvae, including putative stem- and crown-group pancrustaceans with amazing developmental sequences. The putative presence of adult stages remains a source of debate. This causes spurious placements in morphological analyses. We introduce a new method of coding ontogenetic data where each semaphoront (discrete larval or adult stage) is considered an OTU. This decreases the reliance on continuous timing of developmental ‘events’, avoiding a priori assumptions of heterochrony. Characters and states are carefully defined to identify specific putative homologies across taxa, as well as changes in morphology throughout ontogeny. Exemplar taxa from Pancrustacea are included (direct and indirect developers). Phylogenetic analyses of semaphoronts produced relationships of each Orsten fossil to the crown-group clade expected from morphology shared with extant larvae. Bredocaris is a member of the stem lineage of Thecostraca and/or Copepoda, and Yicaris and Rehbachiella are members of the stem lineage of Branchiopoda and/or Cephalocarida. The position of Phosphatocopina remains unresolved. A result consistent with fossil morphology was produced, suggesting this method may have broader applications to other phylogenetic problems that rely on ontogentically variable homology statements.

Although many higher-level relationships throughout the Arthropoda have received congruent support in recent morphological and molecular analyses, a number of nodes remain elusive, particularly within Pancrustacea and Arachnida. In addition to new discoveries (new fossils, new character sources), existing cladistic matrices and morphological images are crucial sources of data for re-interpretation. I present several re-interpretations of historical data resulting in new phylogenetic information. First, using morphological images and descriptions of pancrustacean larval stages to code ontogenetic data into a character matrix where each semaphoront (discrete larval or adult stage) is considered an OTU. This decreases the reliance on continuous timing of developmental ‘events’, while explicitly incorporating previously ignored ontogenetic character changes into phylogenetic analyses. Second, using ontologies (strictly defined vocabularies) to formally define characters across a variety of taxa. This may prove particularly useful in identifying shared character states between Hexapoda and their crustacean sister-group, as many characters that actually are homologous were originally defined in support of a monophyletic Crustacea and sister relationship between Hexapoda and Myriapoda. Ontologies may also be leveraged to construct direct links between gene function (in model organisms) and morphology. Third, nascent technology to automate character coding from high-resolution images and historical dichotomous keys is introduced.

An ambitious, yet fundamental goal for comparative biology is to understand the evolutionary relationships for all of life. Yet many important taxonomic groups have remained recalcitrant to inclusion into broader scale studies. Here, we focus on collection of 9 new 454 transcriptome data sets from Ostracoda, a group that is often under-sampled in broader studies. We combine the new transcriptomes with a new morphological matrix (including fossils) and existing Expressed Sequence Tag (EST), mitochondrial genome, nuclear genome and rDNA data, which leads to new insights into ostracod and pancrustacean phylogeny. We obtained support for three epic pancrustacean clades that likely originated in the Cambrian: Oligostraca (Ostracoda, Mystacocarida, Branchiura, Pentastomida); Multicrustacea (Copepoda, Malacostraca, Thecostraca); and a clade we refer to as Allotriocarida (Hexapoda, Remipedia, Cephalocarida, Branchiopoda). Our support of Allotriocarida is counter to the Vericrustacea hypothesis that puts Branchiopoda with Multicrustacea. Looking within the Oligostraca clade, our results support the unresolved question of ostracod monophyly. Within Multicrustacea, we find support for Thecostraca plus Copepoda, for which we suggest the name Hexanauplia. Within Allotriocarida, some analyses support the hypothesis that Remipedia is the sister taxon to Hexapoda, but others support Brachiopoda+Cephalocarida as the sister group of hexapods. Across hypotheses, we sometimes see better support for equivocal nodes using slow-evolving genes or when excluding distant outgroups, highlighting the increased importance of conditional data combination in this age of abundant, often anonymous data. By concatenating molecular and morphological data, we place pancrustacean fossils in the phylogeny, which can be used for studies of divergence times in Pancrustacea, Arthropoda, or Metazoa. Our results and new data will allow for attributes of Ostracoda, such as its amazing fossil record and diverse biology, to be leveraged in broader scale comparative studies. Further, we illustrate how adding extensive next-generation sequence data from understudied groups can yield important new phylogenetic insights into long-standing questions, especially when carefully analyzed in combination with other data.

Studies of ontogeny have a centuries-long history pioneered by the likes of von Baer, Haeckel, and Darwin. Only in the past 15 years, however, have ontogenetic data been explicitly incorporated into cladistic analyses. However, defining homologous stages across disparate taxa remains problematic. Pancrustaceans undergo some of the most radical ontogenetic changes seen in the Metazoa. They are especially suited to studies of ontogeny as their larval stages are discretely partitioned as moults. The spectacular upper Cambrian ‘Orsten’ fauna (and similar faunas throughout the Phanerozoic) preserve phosphatized fossil larvae, including putative stem- and crown-group pancrustaceans with amazingly complete developmental sequences. The putative presence and nature of adult stages is a source of debate. We introduce a new method of coding ontogenetic data where each semaphoront (discrete larval or adult stage) is considered to be an OTU. This decreases the reliance on continuous timing of developmental ‘events’, and permits a theory-free identification of ontogenetic similarity. Characters and their states are carefully defined to identify specific putative homologies across taxa, as well as changes in morphology throughout ontogeny. We focus in particular on the ontogeny of branchiopods, ostracods, and thecostracans, as some of the best-known Orsten fossils (Rehbachiella, phosphatocopines, and Bredocaris, respectively) have been classified as members of these groups. Exemplar taxa covering most of Pancrustacea were also included. We draw our morphological data mainly from the rich ontogenetic and embryological literature, augmented with some personal observations. This is the first attempt to integrate developmental data from hexapods with other crustaceans, which may provide clues about hexapod affinities and the pattern of character change and ontogenetic evolution leading to terrestrialization. The result demonstrates the complex relationship between ontogeny and phylogeny and sheds light on life cycle evolution.

Arthropod tagmosis is the differentiation of segments along the anterior/posterior axis, producing appendages specialized for sensation, feeding, and locomotion. Characters relating to segment and limb number and morphology are important in constructing phylogenies that include fossil taxa. Chelicerates are a diverse group, including the extant spiders, mites, harvestmen, scorpions, xiphosurans, and the extinct trigonotarbids, eurypterids, chasmataspids, and synziphosurans. The extant pygnogonids (sea spiders) may also belong to this group. The chelicerate body is divided into two major tagmata: prosoma and opisthosoma. There is variation, however, within this bauplan (e.g. number of segments in a limb, fusion of dorsal tergites). Developmentally, patterns of tagmosis are associated with changes in the expression of Hox genes, segment polarity genes, and limb gap genes. The distribution of extant taxa for which Hox expression patterns are known is sparse. Therefore, we studied morphological traits for which the developmental basis is understood in extant chelicerates. We constructed a new phylogeny for chelicerates from over 400 morphological characters. Representative extant taxa with sequence or developmental gene expression data were included, as well as fossils with unique patterns of tagmosis or other morphological traits. Using this morphological topology, ancestral character states were inferred. Results under different models of character evolution (parsimony, likelihood, Bayesian) are compared.

The Pancrustacea (crustaceans plus hexapods) are a riotously speciose, morphologically disparate, and ancient clade of animals. Furthermore, some pancrustaceans, like the Ostracoda, have an outstanding stratigraphic record. Understanding how and when these important animals and their morphologies evolved is a long-standing goal in evolutionary biology, yet their phylogenetic relationships remain controversial. We added new pyrosequencing transcriptome data from 8 disparate ostracod crustaceans to existing EST and mitochondrial genome data, resulting in over 200 gene families analyzed. In addition, we coded more than 150 morphological characters (most previously published), for extant and extinct pancrustaceans. We concatenated all data together for maximum likelihood phylogenetic analyses. Notable preliminary results indicate support for Branchiopoda over Xenocarida as the sister group to Hexapoda; monophyly of Ostracoda (a result never obtained previously with molecular data); monophyly of Oligostraca as the sister group to all other Pancrustacea; and the ancient (Cambrian or earlier) origins of multiple major Pancrustacean groups. The phylogeny of Pancrustacea is likely to remain controversial for some time, but high throughput sequencing technologies are allowing the rapid accumulation of data, which should promote progress toward consensus.

Arthropod tagmosis is the differentiation of segments along the anterior/posterior axis, producing appendages specialized for sensation, feeding, and locomotion. Characters relating to segment and limb number and morphology are important in constructing phylogenies that include fossil taxa. Chelicerates are a diverse group, including the extant spiders, mites, harvestmen, scorpions, xiphosurans, and the extinct trigonotarbids, eurypterids, chasmataspids, and synziphosurans. The extant pygnogonids (sea spiders) may also belong to this group. The chelicerate body is divided into two major tagmata: prosoma and opisthosoma. There is variation, however, within this bauplan (e.g. number of segments in a limb, fusion of dorsal tergites). Developmentally, patterns of tagmosis are associated with changes in the expression of Hox genes. The distribution of extant taxa for which Hox expression patterns are known is sparse. Therefore, we studied morphological traits for which the developmental basis is understood in extant chelicerates. We constructed a new phylogeny for chelicerates from over 400 morphological characters. Representative extant taxa with sequence or developmental gene expression data were included, as well as fossils with unique patterns of tagmosis or other morphological traits. Using this morphological topology, ancestral character states were inferred. Results under different models of character evolution (parsimony, likelihood, Bayesian) are compared.