An overview of the evolution of complex systems of animals

Lecture 1 December 8th, 9:10–9:50
Nori Satoh

Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University (OIST)



Prior to and during the Cambrian explosion, which took place ~540 MYR ago, multicellular animals were likely to be evolved from choanoflagellate-like ancestors. On our planet, at moment, we can see a great variety of animal forms, from sponges and placozoans with less-complex body plans to insects and vertebrates with highly complex body plans. Here I will introduce you a general framework of animal body plans and their evolutionary relationship. General features are explained on diploblasts with radially symmetrical body plans, triploblasts with bilaterally symmetrical body plans, protostomes, deuterostomes and chordates. Tool kits, genetic cascade, and gene regulatory networks, which are involved in the formation of body plans, are also explained to facilitate future discussions on the evolution of complex systems of animals. Finally, several topics of recent evo-devo studies will be discussed in future direction of studies in this field.

Suggested readings

  • Satoh N (2014) Developmental Genomics of Ascidians. Wiley.
  • Satoh N, Rokhsar D, Nishikawa T (2014) Chordate evolution and the three-phylum system. Proc R Soc B 281: 1794.
  • Satoh N et al. (2014) On a possible evolutionary link of the stomochord of hemichordates to pharyngeal organs of chordates. genesis on line.
  • Satoh N, Tagawa K, Takahashi H (2012) How was the notochord born? Evol Dev 14: 56–75.
  • Carroll SB, Grenier JK, Wetherbee SD (2005) From DNA to diversity, 2nd ed.Blackwell Publ.
  • Davidson EH (2006) The regulatory genome. Academic Press.
  • Nielsen C (2012) Animal evolution, 3rd ed. Oxford Univ Press.
  • Arthur W (2011) Evolution: A developmental approach. Wiley-Blackwell Publ.
  • Gilbert S, Epel D (2009) Ecological developmental biology. Sinauer Assoc Inc.


Place of non-bilaterians in the studies of animals evolution and development

Lecture 3 December 9th, 9:30–10:50
Konstantin Khalturin

Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University (OIST)



Cnidarians (sea anemones, corals and jellyfish) represent one of the most basal clades in the phylogenetic tree of the animals kingdom. Due to their diploblastic organization cnidarians are traditionally referred to as "simple" organisms. However it turned out that most of the signal transduction pathways and transcription factors known to play key roles in the embryonic development and axial patterning of much more "complex" bilaterians are also present in the genomes of Nematostella, Hydra and Acropora. This unexpected finding gave rise to a number of questions. Why do morphologically simple organisms need so many genes and why their genome architecture is so complex? How did the last common ancestor of cnidarians and bilaterians look like? In my lecture I will summarize the contribution of cnidarian model systems to our current understanding of how animal genomes and developmental mechanisms evolve.

Suggested readings

  • Kortschak RD et al. (2003) EST analysis of the cnidarian Acropora millepora reveals extensive gene loss and rapid sequence divergence in the model invertebrates. Curr Biol 13: 2190–2195.
  • Putnam NH et al. (2007) Sea anemone genome reveals ancestral eumetazoan gene repertoire and genome organization. Science 317: 86–94.
  • Technau U, Steele RE (2011) Evolutionary crossroads in developmental biology: Cnidaria. Development 138: 1447–1458.
  • Shinzato C et al. (2011) Using the Acropora digitifera genome to understand coral responses to environmental change. Nature 476: 320–3.
  • Steinmetz PR et al. (2012) Independent evolution of striated muscles in cnidarians and bilaterians. Nature 487: 231–234.



Development and evolution of arthropod diversity

Lecture 4 December 9th, 13:10–14:30
Nipam H. Patel

Dept. of Molecular and Cell Biology and Dept. of Integrative Biology, University of California, Berkeley



The arthropod phylum contains the greatest number of described species within the animal kingdom, and these species show a remarkable level of morphological and developmental diversity. The arthropod body plan is composed of repeating segments, with most of these segments possessing a unique morphology and distinctive pair of appendages. I will discuss how this body plan is established during development, relying primarily upon the knowledge from Drosophila (fruit fly) development. Starting with this information, we have been able to expand to several emerging model systems, including the amphipod crustacean Parhyale, to understand how evolution has altered development to create morphological diversity. I will also describe the remarkable ability of Parhyale to replace its germline, and the development and evolution of butterfly wings and the remarkable process that allows them to generate color through structure rather than pigment.

Suggested readings

  • Dinwiddie A, Null R, Pizzano M, Chuong L, Leigh Krupp A, Ee Tan H, Patel NH (2014) Dynamics of F-actin prefigure the structure of butterfly wing scales. Dev Biol 392: 404–418.
  • Vargas-Villa MA, Hannibal RL, Parchem RJ, Liu PZ, Patel NH (2010) A prominent requirement for single-minded and the ventral midline in patterning the dorsoventral axis of the crustacean Parhyale hawaiensis. Development 137: 3469–3476.
  • Liubicich DM, Serano J, Pavlopoulos A, Kontarakis Z, Protas ME, Kwan E, Chatterjee S, Tran KD, Averof M, Patel N (2009) Knockdown of Parhyale Ultrabithorax recapitulates evolutionary changes in crustacean appendage morphology. PNAS 106: 13892–13896.
  • Vukusic P, Sambles JR, Lawrence CR (2000) Colour mixing in wing scales of a butterfly. Nature 404: 457.




Transcriptional precision in the Drosophila embryo and the evolutionary origins of the vertebrate head in the Ciona tadpole

Lecture 5 December 10th, 9:00–10:20
Mike Levine

Center for Integrative Genomics, University of California, Berkeley



The first half of my lecture will be devoted to mechanisms of gene regulation in the early Drosophila embryo. This system is ideally suited for the visualization of gene activity in development since the embryo is composed of ~6,000 nuclei arranged as a monolayer at the surface of the egg. These nuclei display fast and furious expression of key patterning genes during a period of less than an hour, resulting in localized stripes and bands of gene expression that establish the basic blueprint of the adult fly. I will emphasize the importance of transcriptional enhancers in establishing these patterns of gene expression, and present our first efforts to observe enhancer-promoter communication in living embryos. The second half of my lecture will focus on the anterior neural plate of the Ciona embryo. This region of the embryo contains several cell types evocative of the cranial neural crest and placodes in vertebrates. I will present evidence for an olfactory progenitor cell that has mixed properties of chemosensory cells and migrating GnRH-expressing neurons. I will also present a controversial model for the evolutionary origins of vertebrate neural crest.

Suggested readings

  • Levine M (2010) Transcriptional enhancers in animal development and evolution. Curr Biol 20: R754–763.
  • Lagha M, Bothma JP, Esposito E, Ng S, Stefanik L, Tsui C, Johnston J, Chen K, Gilmour DS, Zeitlinger J, Levine M (2013) Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo. Cell 153: 976–987.
  • Abitua PB, Wagner E, Navarrete IA, Levine M (2012) Identification of a rudimentary neural crest in a non-vertebrate chordate. Nature 492: 104–107.



Complexity of developmental regulation – Lessons from sea urchins

Lecture 6 December 11th, 9:00–10:20
Yi-Hsien Su

Institute of Cellular and Organismic Biology (ICOB), Academia Sinica



Sea urchins have been a research model in developmental biology for over a century. Single-cell thickness structures of their embryos provide a great tool for understanding complexity of developmental mechanisms. Gene regulatory network (GRN) studies in sea urchin embryos describe the causal links between genomic regulatory sequences and regulatory factors and explain mechanistically how a pregastrular embryo forms from a fertilized egg. After the initial specification by maternal factors, massive intercellular signals increase spatial complexity and transform the radial symmetric pregastrula to a bilateral symmetric gastrula, then a left-right asymmetric larva, and eventually to a pentasymmetric body plan that is characteristic to the phylum Echinodermata. The published sea urchin developmental GRNs encompass specification processes of ectoderm, endoderm, and mesoderm. Efforts have also been made to extend GRN analyses to axial patterning, morphogenesis, and cell differentiation. Comparative studies on sea urchins and their echinoderm allies also provide clues for understanding how GRNs are shaped during evolution. I will discuss recent discoveries related to these topics.

Suggested readings

  • McClay DR (2011) Evolutionary crossroads in developmental biology: sea urchins. Development 138: 2639–2648.
  • Luo YJ, Su YH (2012) Opposing Nodal and BMP signals regulate left-right asymmetry in the sea urchin larva. PLOS Biol 10(10): e1001402. doi:10.1371/journal.pbio.1001402.
  • Ben-Tabou de-Leon S, Su YH, Lin, KT, Li E, Davidson EH (2013) Gene regulatory control in the sea urchin aboral ectoderm: Spatial initiation, signaling inputs, and cell fate lockdown. Dev Biol 374: 245–254.
  • Yankura KA, Koechlein CS, Cryan AF, Cheatle A, Hinman VF (2013) Gene regulatory network for neurogenesis in a sea star embryo connects broad neural specification and localized patterning. PNAS 110: 8591–8596.




Lecture 7 December 11th, 10:40–12:00
Chris Lowe

Hopkins Marine Station, Stanford University



I will broadly focus on body plan evolution of the major deuterostome phyla and the utility of body patterning genes in the reconstruction of both ancestral morphologies and developmental strategies. The work in my lab has largely focused on characterizing the early development of the direct-developing enteropneust Saccoglossus kowalevskii as a representative of hemichordates to compare with chordate and echinoderms. I will present data on the establishment of the anteroposterior axis and discuss how functional analyses of the Wnt and Nodal signaling pathways reveal both conserved and potentially evolutionarily derived roles. In the final part of the talk I will advocate for a comparative developmental approach that incorporates the diversity of life history strategies that are particularly diverse in deuterostome phyla.

Suggested readings

  • Darras S et al., (2011) β-Catenin specifies the endomesoderm and defines the posterior organizer of the hemichordate Saccoglossus kowalevskii. Development 138: 959–970.
  • Lowe CJ et al. (2003) Anteroposterior patterning in hemichordates and the origins of the chordate nervous system. Cell 113: 853–865.
  • Pani AM et al. (2012) Ancient deuterostome origins of vertebrate brain signaling centres. Nature 483: 289–294.



Basal chordate amphioxus and the origin of vertebrates

Lecture 8 December 11th, 13:30–14:50
Jr-Kai Sky Yu

Institute of Cellular and Organismic Biology, Academia Sinica



The phylum Chordata includes three subphyla: Cephalochordata (amphioxus or lancelets), Tunicata (ascidians, appendicularians and thaliaceans) and Vertebrata (gnathostomes plus agnathans). Amphioxus and tunicates are invertebrates that are grouped with vertebrates in the chordate phylum because of shared features that include the dorsal nerve chord, notochord, segmented somites, and pharyngeal gill slits. Amphioxus was traditionally held to be the closest invertebrate chordate relative of the vertebrates, but recent molecular phylogenetic analyses have put tunicates as the sister-taxon of vertebrates and considered amphioxus as the most basal chordate group. Nevertheless, compared to tunicates, amphioxus appears to have preserved more ancestral characteristics after its divergence from other chordate lineages. Here, I will review the recent advances in comparative developmental studies between amphioxus and vertebrates, and I will also discuss their implications for the evolutionary origin of vertebrates.

Suggested readings

  • Putnam NH et al. (2008) The amphioxus genome and the evolution of the chordate karyotype. Nature 453: 1064–1071.
  • Yu JKS (2010) The evolutionary origin of the vertebrate neural crest and its developmental gene regulatory network - insights from amphioxus. Zoology 113: 1–9.
  • Bertrand S, Escriva H (2011) Evolutionary crossroads in developmental biology: amphioxus. Development 138: 4819–4830.



Coupling Hox genes to head development in chordate evolution: A story in segments

Lecture 10 December 12th, 9:30–10:50
Robb Krumlauf

Stowers Institute for Medical Research (SIMR), Kansas City Missouri, USA



The vertebrate hindbrain and its relationship to head development is a good model system for understanding fundamental mechanisms of patterning and morphogenesis during development, disease and evolution. The vertebrate hindbrain is a highly conserved co-ordination center of the CNS where regional diversity and patterning of neurogenesis is achieved through a process of segmentation which ultimately gives rise to well-defined regions of the adult brain. The Hox family of transcription factors is coupled to this process and provides a molecular framework for specifying the unique identities of hindbrain segments and developing neurons. Because the segmental processes of head development are highly conserved among vertebrates, comparative studies between different species have greatly enhanced our ability to build a picture of the regulatory cascades that control early head development. Through comparative studies in lamprey, zebrafish and mice we are beginning to address the question of when ordered domains of Hox expression were coupled to hindbrain segmentation in chordate origins. Very little is known about how Hox proteins control downstream target genes to fulfill their roles in the CNS. To identity potential target genes on a genome wide basis, we have used mouse tissues and programmed differentiation of mouse ES cells in combination with ChIP-Seq technology. Genomic analyses have uncovered novel properties of Hox proteins that underlie their functional roles. This lecture will discuss current understanding of the pathways that govern patterning of the vertebrate head, how these pathways are conserved in evolution and properties of Hox proteins.

Suggested readings

  • Alexander T, Nolte C, Perryn E, Krumlauf R (2009) Hox genes and vertebrate segmentation. In: Annual Review of Cell and Developmental Biology 25: 431–456.
  • Tümpel S, Wiedemann LM, Krumlauf R (2009) Hox genes and segmentation of the vertebrate hindbrain. In: Cur Topics in Dev Biol, Pourquie O (ed), AP 88: 103–113.
  • Parker H, Bronner M, Krumlauf R (2014) A Hox regulatory network for hindbrain segmentation is conserved to the base of vertebrates. Nature 514: (In press) http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13723.html?WT.ec_id=NATURE-20140918



Genome sequencing and vertebrate innovations: looking for new stuff using comparative genomic approaches

Lecture 11 December 12th, 13:10–14:30
Chris Amemiya

Benaroya Research Institute & Department of Biology, University of Washington, Seattle, Washington, USA



Genome assemblies are being reported for a plethora of animal species and thousands will be generated over the course of the next few years as part of the international Genome 10K efforts. Many (if not most) genome papers submitted today are largely formulaic and descriptive, and the biological content in these reports is sometimes embarrassingly low and wildly over-interpreted. Genomics can only take us so far without the proper authentication via biology. Here, I will discuss some recent genome efforts in my lab (lamprey, coelacanth) whereby novel characteristics of the genomes can be exploited to learn about interesting and hitherto uninvestigated biological problems. My thesis is that, while comparisons of the “known” genetic components between species are important and necessary, many salient evo-devo insights will be gotten only when specifically looking for the differences. I will give a couple of examples, including one that suggests a new mechanism for cellular and developmental programming based on the use of glycopolymers, “glyco-evo-devo.”

Suggested readings

  • Amemiya CT, Saha NR, Zapata AG (2007) Evolution and development of immunological structures in the lamprey. Curr Opinion Immunol 19: 535–541.
  • Amemiya CT et al. (2010) Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome. PNAS 107: 3622–3627.
  • Amemiya CT et al. (2013) The African coelacanth genome provides insights into tetrapod evolution. Nature 496: 311–316.
  • Amemiya CT et al. (2014) The African coelacanth and its genome and companion papers for the coelacanth genome. J Exptl Zool (MDE), OPEN ACCESS: http://onlinelibrary.wiley.com/doi/10.1002/jez.b.v322.6/issuetoc
  • Pancer Z, Amemiya CT, Ehrhardt GRA, Ceitlin J, Gartland GL, Cooper MD (2004) Somatic diversification of variable lymphocyte receptors in the agnathan sea lamprey. Nature 430: 174–180.
  • Smith JJ, Antonacci F, Eichler EE, Amemiya CT (2009) Programmed loss of millions of base pairs from a vertebrate genome. PNAS 106: 11212–11217.
  • Smith JJ, Baker C, Eichler EE, Amemiya CT (2012) Genetic consequences of programmed genome rearrangement. Curr Biol 22: 1524–1529.
  • Smith JJ et al. (2013) Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nat Genet 45: 415–421.



What can Xenoturbella development tell us about the evolution of marine invertebrate larvae?

Short talk 1 December 9th, 11:10–11:50
Hiroaki Nakano

Shimoda Marine Research Center, University of Tsukuba, JAPAN



Xenoturbella is a worm-like marine animal about 1-3 cm long possessing a simple body plan. It lacks a through gut, gonads, coelomic cavities, and brain. Its nervous system is a diffuse nerve net with no centralization. Due to the simple body plan, its phylogenetic position has long remained obscure. Recent phylogenomic analyses suggest that it forms a new phylum, the Xenacoelomorpha, together with the Acoelomorpha. However, the phylogenetic position of the phylum is still undecided, either as an early branching bilaterian or as a sister group to the Ambulacraria (hemichordates and echinoderms) within the deuterostomes. Developmental studies that may provide data to help resolve this problem have been performed on a number of acoel species, but Xenoturbella development had long remained a mystery. I have succeeded in making the first observations of spawned gametes and developmental stages from this animal since it was first discovered in 1878. Xenoturbella possess swimming hatchlings similar to the free-swimming stages of some acoels and to the cnidarian planula larva. The phylogenetic position of Xenacoelomorpha will be discussed through comparisons of Xenoturbella gametes and developmental stages with those of basal metazoans, acoels and deuterostomes. Developmental patterns of the metazoan and deuterostome ancestor and evolution of metazoan larvae will also be discussed based on the new observations on Xenoturbella.



Molluscan-specific genes at synapse and brain

Short talk 2 December 9th, 15:50–16:30
Masa-aki Yoshida

JSPS postdoctoral research fellow, National Institute of Genetics, JAPAN The Whitney laboratory for Marine Bioscience, University of Florida, USA

Leonid L. Moroz

Dept of Neuroscience and The Whitney laboratory for Marine Bioscience, University of Florida, USA



The sea slug Aplysia carifornica have been a well-established model organism for cellular and molecular neurobiology. The gigantic neurons and simpler nervous system have advantages to analyze cellular and genomic mechanisms such as synaptic plasticity during learning and memory formation. To overview the activity of all the genes in identified neurons as they ‘learn and remember’, our group applied massive sequencing approaches including single-neuron RNA-Seq and annotated results using the recently assembled Aplysia genome. Here, we focused on cell adhesion molecules to characterize their diversity and function in neural circuits as well as evolution of this superfamily in molluscs. Previously, the Aplysia cell adhesion molecule (apCAM) was well studied to be associated with structural changes of the synapses during long-term memory formation. The homologs, vertebrate NCAM and Drosophila Fasciclin2 are also involved in the memory formation. However, our analysis highlighted hundreds of new genes that changed their expression during two chemically induced models of memory consolidation. Specifically, we found a new memory-related gene, NCAML1. The gene encodes a GPI-linked adhesion molecule. Phylogenetic analysis revealed that the NCAML1 originated from Neuroglian in the molluscan lineage and was specifically found in molluscan species. The analysis also provided many additional Molluscan-specific genes responsible for the memory consolidation processes. The single-neuron RNA-Seq also revealed differential expression of numerous adhesion molecules between sensory and motor neurons in memory circuits. Each cell has a distinct expression pattern of transcription factors, which could also reflect the state of activity and/or cellular identity. These findings open unique opportunities to study genomic bases of neural identity in the broad evolutionary context. In addition, we’re now focusing on cephalopod molluscs, octopuses, squids and nautiloids, and the abilities to maintain complex memory such as visual tactics. Their brain appears to have been evolved from the molluscan common ancestor with a diffuse like nerve system in the form of tetraneury with several independent examples of centralization. We will briefly report our genome projects targeting comparative genomics across the molluscs.

Suggested readings

  • Moroz LL et al. 2006. Neuronal transcriptome of Aplysia: neuronal compartments and circuitry. Cell 127: 1453–1467.



The Lingula genome and the evolution of lophotrochozoans and biomineralization

Short talk 3 December 9th, 16:30–17:10
Yi-Jyun Luo

Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University (OIST)



In contrast to left-right and calcium carbonate shells of bivalves, the “living fossil” brachiopod Lingula anatina has dorsal-ventral shells made of collagen fibers and calcium phosphate, and its embryonic development exhibits deuterostomy features. The evolutionary origins of brachiopods and their chitinophosphatic shells are unclear. In addition, their phylogenetic position in lophotrochozoans is highly debated. Here we sequenced the draft genome of Lingula by Roche 454, Illumina, and PacBio platforms in approximately 234-fold coverage, together with adult tissue and developmental transcriptomes as well as a shell matrix proteome. Our data based on comprehensive phylogenomic analyses place Lingula as the sister to Mollusca and show its slowest evolutionary rate among lophotrochozoans. This hypothesis is further supported by intron structure and microsynteny analyses. Furthermore, Hox gene cluster is disorganized without spatial or temporal colinearity and lox2 and lox4 genes are missing. Further analyses on gene family evolution show that there is high turnover rate of gene family gain and loss. These data suggest that despite of the fact that core eukaryotic gene sets in Lingula genome evolve slowly, the genome has changed dynamically and rapidly rather than a slowly changed “living fossil.” Intriguingly, although Lingula and vertebrates share similar hard tissue components, genomic scale analyses of bone formation genes and fibrillar collagen family indicate that Lingula lacks the important gene sets in the vertebrate bone formation and has a new group of shell matrix collagens with novel structure carrying EGF-like domain. Moreover, by analyses of genomic architecture and gene phylogeny, we show that four shell matrix proteins are probably acquired from bacteria via horizontal gene transfer. Taken together, our results suggest that mineralized tissues with the features of fibrillar collagen and calcium phosphate shared by Lingula and vertebrates might be the result of convergent evolution.



Hox genes in ascidians

Short talk 4 December 11th, 16:50–17:30
Hidetoshi Saiga

Tokyo Metropolitan University, JAPAN



Hox genes play a key role in establishing the animal body plan. Hox genes are often characterized by their genomic structure to form a cluster on the chromosome and their expression pattern along the anterior-posterior axis in a coordinated manner with the gene order on the chromosome. Ascidians are members of urochordates, closest extant animals to vertebrates. Nevertheless, they exhibit rather unique development, forming tadpole larvae with a basal chordate body plan, followed by metamorphosis to sessile adults. How is this unique development reflected in the structure, expression and function of Hox genes? In the ascidian, Ciona intestinalis, 9 Hox genes have been identified and found located on 2 chromosomes. The expression patterns in the development have been examined, which revealed that 7 genes are expressed up to the larval stage. These Hox genes seem to play a rather limited role up to the larval development, except that a few genes such as Hox12 and Hox10 play a critical role in the larval tail morphogenesis and gut formation, respectively. Based on these observations, putative characteristics of Hox genes in ascidians will be discussed.



Is the hourglass model, unified theory of Evo-Devo?

Short talk 5 December 12th, 14:50–15:30
Naoki Irie

University of Tokyo, Japan, JAPAN



Are there general, unified relationship between animal embryogenesis and their evolution? It’s one of the long-standing questions in the field of Evo-Devo, since the era of Ernst Haeckel, however, it has been left un-integrated to modern biology until recently. Based on mechanistic point of view, it would be reasonable to assume that earlier embryonic stages become evolutionarily conserved because these are the stages when fundamental anatomical features (e.g. body axis, segmentation, specification of segmented structures) are established. In other words, changes in earlier developmental processes would have higher chance of becoming lethal, and this in turn makes earlier stages more difficult to change during evolution (= conserved). Contrary to this idea, recent transcriptomic studies found that rather than the earliest, but mid-embryonic stages are the most conserved stages, supporting the “developmental hourglass model”. This has been shown in arthropods, vertebrates, and nematodes, however, many questions remain to be answered. Especially, why this mid-embryonic stage has to be conserved throughout hundreds of millions of years in evolution? Does this have to do with robustness and/or fragileness of embryogenesis? By briefly overviewing our recent findings, together with other studies in this field, I would like to int