Patterns and consequences of vertebrate Emx gene duplications

Evolution of Telencephalon Anterior-Posterior Patterning through Core Endogenous Network Bifurcation

How did the complex structure of the telencephalon evolve? Existing explanations are based on phenomena and lack a first-principles account. The Darwinian dynamics and endogenous network theory-established decades ago-provides a mathematical and theoretical framework and a general constitutive structure for theory-experiment coupling for answering this question from a first-principles perspective. By revisiting a gene network that explains the anterior-posterior patterning of the vertebrate telencephalon, we found that upon increasing the cooperative effect within this network, fixed points gradually evolve, accompanied by the occurrence of two bifurcations. The dynamic behavior of this network is informed by the knowledge obtained from experiments on telencephalic evolution. Our work provides a quantitative explanation for how telencephalon anterior-posterior patterning evolved from the pre-vertebrate chordate to the vertebrate and provides a series of verifiable predictions from a first-principles perspective.

Forebrain Architecture and Development in Cyclostomes, with Reference to the Early Morphology and Evolution of the Vertebrate Head

The vertebrate head and brain are characterized by highly complex morphological patterns. The forebrain, the most anterior division of the brain, is subdivided into the diencephalon, hypothalamus, and telencephalon from the neuromeric subdivision into prosomeres. Importantly, the telencephalon contains the cerebral cortex, which plays a key role in higher order cognitive functions in humans. To elucidate the evolution of the forebrain regionalization, comparative analyses of the brain development between extant jawed and jawless vertebrates are crucial. Cyclostomes - lampreys and hagfishes - are the only extant jawless vertebrates, and diverged from jawed vertebrates (gnathostomes) over 500 million years ago. Previous developmental studies on the cyclostome brain were conducted mainly in lampreys because hagfish embryos were rarely available. Although still scarce, the recent availability of hagfish embryos has propelled comparative studies of brain development and gene expression. By integrating findings with those of cyclostomes and fossil jawless vertebrates, we can depict the morphology, developmental mechanism, and even the evolutionary path of the brain of the last common ancestor of vertebrates. In this review, we summarize the development of the forebrain in cyclostomes and suggest what evolutionary changes each cyclostome lineage underwent during brain evolution. In addition, together with recent advances in the head morphology in fossil vertebrates revealed by CT scanning technology, we discuss how the evolution of craniofacial morphology and the changes of the developmental mechanism of the forebrain towards crown gnathostomes are causally related.

The Independent Evolution of Dorsal Pallia in Multiple Vertebrate Lineages

Comparative neurobiologists have long wondered when and how the dorsal pallium (e.g., mammalian neocortex) evolved. For the last 50 years, the most widely accepted answer has been that this structure was already present in the earliest vertebrates and, therefore, homologous between the major vertebrate lineages. One challenge for this hypothesis is that the olfactory bulbs project throughout most of the pallium in the most basal vertebrate lineages (notably lampreys, hagfishes, and lungfishes) but do not project to the putative dorsal pallia in teleosts, cartilaginous fishes, and amniotes (i.e., reptiles, birds, and mammals). To make sense of these data, one may hypothesize that a dorsal pallium existed in the earliest vertebrates and received extensive olfactory input, which was subsequently lost in several lineages. However, the dorsal pallium is notoriously difficult to delineate in many vertebrates, and its homology between the various lineages is often based on little more than its topology. Therefore, we suspect that dorsal pallia evolved independently in teleosts, cartilaginous fishes, and amniotes. We further hypothesize that the emergence of these dorsal pallia was accompanied by the phylogenetic restriction of olfactory projections to the pallium and the expansion of inputs from other sensory modalities. We do not deny that the earliest vertebrates may have possessed nonolfactory sensory inputs to some parts of the pallium, but such projections alone do not define a dorsal pallium.

The evolutionary origins of the vertebrate olfactory system

Vertebrates develop an olfactory system that detects odorants and pheromones through their interaction with specialized cell surface receptors on olfactory sensory neurons. During development, the olfactory system forms from the olfactory placodes, specialized areas of the anterior ectoderm that share cellular and molecular properties with placodes involved in the development of other cranial senses. The early-diverging chordate lineages amphioxus, tunicates, lampreys and hagfishes give insight into how this system evolved. Here, we review olfactory system development and cell types in these lineages alongside chemosensory receptor gene evolution, integrating these data into a description of how the vertebrate olfactory system evolved. Some olfactory system cell types predate the vertebrates, as do some of the mechanisms specifying placodes, and it is likely these two were already connected in the common ancestor of vertebrates and tunicates. In stem vertebrates, this evolved into an organ system integrating additional tissues and morphogenetic processes defining distinct olfactory and adenohypophyseal components, followed by splitting of the ancestral placode to produce the characteristic paired olfactory organs of most modern vertebrates.

The expression of FoxG1 in the early development of the European river lamprey Lampetra fluviatilis demonstrates significant heterochrony with that in other vertebrates

FoxG1, a member of the Fox/Forkhead family of winged helix transcription factors, plays key roles in the induction and spatial compartmentalization of the telencephalon in vertebrates. Loss- and gain-of-function experiments have established FoxG1 as a maintenance factor for neural progenitors and a crucial player in the specification of the ventral telencephalon (subpallium). For the first time in evolution, the telencephalon appeared in the ancestors of vertebrates, including cyclostomes. However, although FoxG1 homologues are present in cyclostomes (i.e., in lampreys and hagfishes), no systematic study of the spatial-temporal expression of FoxG1 during the embryonic development of these animals has been carried out. Given these findings, we have now studied FoxG1 spatial-temporal expression patterns in the early development of the European river lamprey Lampetra fluviatilis. We show that in contrast to other vertebrates, in which the expression of FoxG1 begins during neurulation, the expression of this gene in L. fluviatilis starts after neurulation, first at stage 21 (early head protrusion) in the area of the otic placodes and then, beginning from stage 22, in the telencephalon. Such heterochrony of FoxG1 expression in the lamprey may reflect the fact that in this basally divergent representative of vertebrates, telencephalon specification occurs relatively late. This heterochrony could be related to the evolutionary history of the telencephalon, with a recent appearance in vertebrates as an extension to more ancient anterior brain regions. Another peculiarity of FoxG1 expression in lamprey, compared to other vertebrates, is that it is not expressed in the lamprey optic structures.

Inference of the ancestral vertebrate phenotype through vestiges of the whole-genome duplications

Inferring the phenotype of the last common ancestor of living vertebrates is a challenging problem because of several unresolvable factors. They include the lack of reliable out-groups of living vertebrates, poor information about less fossilizable organs and specialized traits of phylogenetically important species, such as lampreys and hagfishes (e.g. secondary loss of vertebrae in adult hagfishes). These factors undermine the reliability of ancestral reconstruction by traditional character mapping approaches based on maximum parsimony. In this article, we formulate an approach to hypothesizing ancestral vertebrate phenotypes using information from the phylogenetic and functional properties of genes duplicated by genome expansions in early vertebrate evolution. We named the conjecture as ‘chronological reconstruction of ohnolog functions (CHROF)’. This CHROF conjecture raises the possibility that the last common ancestor of living vertebrates may have had more complex traits than currently thought.

The Shark Basal Hypothalamus: Molecular Prosomeric Subdivisions and Evolutionary Trends

The hypothalamus is a key integrative center of the vertebrate brain. To better understand its ancestral morphological organization and evolution, we previously analyzed the segmental organization of alar subdivisions in the catshark Scyliorhinus canicula, a cartilaginous fish and thus a basal representative of gnathostomes (jawed vertebrates). With the same aim, we deepen here in the segmental organization of the catshark basal hypothalamus by revisiting previous data on ScOtp, ScDlx2/5, ScNkx2.1, ScShh expression and Shh immunoreactivity jointly with new data on ScLhx5, ScEmx2, ScLmx1b, ScPitx2, ScPitx3a, ScFoxa1, ScFoxa2 and ScNeurog2 expression and proliferating cell nuclear antigen (PCNA) immunoreactivity. Our study reveals a complex genoarchitecture for chondrichthyan basal hypothalamus on which a total of 21 microdomains were identified. Six belong to the basal acroterminal region, the rostral-most point of the basal neural tube; seven are described in the tuberal region (Tu/RTu); four in the perimamillar region (PM/PRM) and four in the mamillar one (MM/RM). Interestingly, the same set of genes does not necessarily describe the same microdomains in mice, which in part contributes to explain how forebrain diversity is achieved. This study stresses the importance of analyzing data from basal vertebrates to better understand forebrain diversity and hypothalamic evolution.

The Lamprey Pallium Provides a Blueprint of the Mammalian Layered Cortex

The basic architecture of the mammalian neocortex is remarkably similar across species. Pallial structures in the reptilian brain are considered amniote precursors of mammalian neocortex, whereas pallia of anamniotes ("lower" vertebrates) have been deemed largely insignificant with respect to homology. Here, we examine the cytoarchitecture of the lateral pallium in the lamprey, the phylogenetically oldest group of extant vertebrates. We reveal a three-layered structure with similar excitatory cell types as in the mammalian cortex and GABAergic interneurons. The ventral parts are sensory areas receiving monosynaptic thalamic input that can be activated from the optic nerve, whereas the dorsal parts contain motor areas with efferent projections to the brainstem, receiving oligosynaptic thalamic input. Both regions receive monosynaptic olfactory input. This three-layered "primordial" lamprey lateral pallium has evolved most features of the three-layered reptilian cortices and is thereby a precursor of the six-layered "neo" cortex with a long-standing evolutionary precedent (some 500 million years ago).

Emx1 Is Required for Neocortical Area Patterning

Establishing appropriate area patterning in the neocortex is a critical developmental event, and transcription factors whose expression is graded across the developing neural axes have been implicated in this process. While previous reports suggested that the transcription factor Emx1 does not contribute to neocortical area patterning, those studies were performed at perinatal ages prior to the emergence of primary areas. We therefore examined two different Emx1 deletion mouse lines once primary areas possess mature features. Following the deletion of Emx1, the frontal and motor areas were expanded while the primary visual area was reduced, and overall the areas shifted posterio-medially. This patterning phenotype was consistent between the two Emx1 deletion strategies. The present study demonstrates that Emx1 is an area patterning transcription factor and is required for the specification of the primary visual area.

Evidence from cyclostomes for complex regionalization of the ancestral vertebrate brain

The vertebrate brain is highly complex, but its evolutionary origin remains elusive. Because of the absence of certain developmental domains generally marked by the expression of regulatory genes, the embryonic brain of the lamprey, a jawless vertebrate, had been regarded as representing a less complex, ancestral state of the vertebrate brain. Specifically, the absence of a Hedgehog- and Nkx2.1-positive domain in the lamprey subpallium was thought to be similar to mouse mutants in which the suppression of Nkx2-1 leads to a loss of the medial ganglionic eminence. Here we show that the brain of the inshore hagfish (Eptatretus burgeri), another cyclostome group, develops domains equivalent to the medial ganglionic eminence and rhombic lip, resembling the gnathostome brain. Moreover, further investigation of lamprey larvae revealed that these domains are also present, ruling out the possibility of convergent evolution between hagfish and gnathostomes. Thus, brain regionalization as seen in crown gnathostomes is not an evolutionary innovation of this group, but dates back to the latest vertebrate ancestor before the divergence of cyclostomes and gnathostomes more than 500 million years ago.

Evolution and functional diversity of aquaporins

In this review, we provide a brief synopsis of the evolution and functional diversity of the aquaporin gene superfamily in prokaryotic and eukaryotic organisms. Based upon the latest data, we discuss the expanding list of molecules shown to permeate the central pore of aquaporins, and the unexpected diversity of water channel genes in Archaea and Bacteria. We further provide new insight into the origin by horizontal gene transfer of plant glycerol-transporting aquaporins (NIPs), and the functional co-option and gene replacement of insect glycerol transporters. Finally, we discuss the origins of four major grades of aquaporins in Eukaryota, together with the increasing repertoires of aquaporins in vertebrates.

Reevaluating Emx gene phylogeny: homopolymeric amino acid tracts as a potential factor obscuring orthology signals in cyclostome genes

BACKGROUND

Vertebrate Emx genes, retained as multiple copies, are expressed in a nested pattern in the early embryonic forebrain and required for its regionalization. This pattern seems to have originated in a vertebrate common ancestor; however, a previous analysis, reporting two lamprey Emx genes, claimed independent Emx gene duplications in both cyclostome (extant jawless fish) and gnathostome (jawed vertebrate) lineages after their divergence. This scenario is neither parsimonious nor consistent with the hypothesis that genome expansion occurred before the cyclostome-gnathostome split, which is supported by recent genome-wide analyses.

RESULTS

We isolated and sequenced cDNA of two hagfish Emx genes and performed intensive molecular phylogenetic analyses, including the hagfish and/or lamprey Emx genes. The lamprey genes tended to attract each other in inferred phylogenetic trees, an effect that tended to be relaxed on inclusion of the hagfish genes. The results of these analyses suggest that cyclostome EmxB is orthologous to gnathostome Emx2, which was also supported by conserved synteny. Homopolymeric amino acid (HPAA) tracts represent a remarkable feature of the lamprey Emx sequences, and a comparative genome-wide scan revealed that lamprey proteins exhibit a unique pattern of HPAA tract accumulation.

CONCLUSIONS

Our analysis, including hagfish Emx genes, suggests that gene duplications gave rise to Emx1, -2 and -3 before the cyclostome-gnathostome split. We propose that independent HPAA tract accumulations in multiple ancient duplicates, as identified in lamprey Emx gene products, may have led to erroneous identification of gene duplication in the lamprey lineage. Overall, our reanalysis favors the scenario that the nested Emx expression pattern in mouse and lamprey shares a common origin.

Evolution of the regionalization and patterning of the vertebrate telencephalon: what can we learn from cyclostomes?

The telencephalon, the most anterior part of the vertebrate central nervous system (CNS), is a highly diversified region of the vertebrate body. Its evolutionary origin remains elusive, especially with regard to the ancestral state of its architecture as well as the origin of telencephalon-specific neuron subtypes. Cyclostomes (lampreys and hagfish), the sister group of the gnathostomes (jawed vertebrates), serve as valuable models for studying the evolution of the vertebrate CNS. Here, we summarize recent studies on the development of the telencephalon in the lamprey. By comparing detailed developmental studies in mammals, we illustrate a possible ancestral developmental plan underlying the diversification of the vertebrate telencephalon and propose possible approaches for understanding the early evolution of the telencephalon.

Piscine aquaporins: an overview of recent advances

Aquaporins are a superfamily of integral membrane proteins that facilitate the rapid and yet highly selective flux of water and other small solutes across biological membranes. Since their discovery, they have been documented throughout the living biota, with the majority of research focusing on mammals and plants. Here, we review available data for piscine aquaporins, including Agnatha (jawless fish), Chondrichthyes (chimaeras, sharks, and rays), Dipnoi (lungfishes), and Teleostei (ray-finned bony fishes). Recent evidence suggests that the aquaporin superfamily has specifically expanded in the chordate lineage consequent to serial rounds of whole genome duplication, with teleost genomes harboring the largest number of paralogs. The selective retention and dichotomous clustering of most duplicated paralogs in Teleostei, with differential tissue expression profiles, implies that novel or specialized physiological functions may have evolved in this clade. The recently proposed new nomenclature of the piscine aquaporin superfamily is discussed in relation to the phylogenetic signal and genomic synteny, with the teleost aquaporin-8 paralogs used as a case study to illustrate disparities between the underlying codons, molecular phylogeny, and physical locus. Structural data indicate that piscine aquaporins display similar channel restriction residues found in the tetrapod counterparts, and hence their functional properties seem to be conserved. However, emerging evidence suggests that regulation of aquaporin function in teleosts may have diverged in some cases. Cell localization and experimental studies imply that the physiological roles of piscine aquaporins extend at least to osmoregulation, reproduction, and early development, although in most cases their specific functions remain to be elucidated.

Genome biology of the cyclostomes and insights into the evolutionary biology of vertebrate genomes

The jawless vertebrates (lamprey and hagfish) are the closest extant outgroups to all jawed vertebrates (gnathostomes) and can therefore provide critical insight into the evolution and basic biology of vertebrate genomes. As such, it is notable that the genomes of lamprey and hagfish possess a capacity for rearrangement that is beyond anything known from the gnathostomes. Like the jawed vertebrates, lamprey and hagfish undergo rearrangement of adaptive immune receptors. However, the receptors and the mechanisms for rearrangement that are utilized by jawless vertebrates clearly evolved independently of the gnathostome system. Unlike the jawed vertebrates, lamprey and hagfish also undergo extensive programmed rearrangements of the genome during embryonic development. By considering these fascinating genome biologies in the context of proposed (albeit contentious) phylogenetic relationships among lamprey, hagfish, and gnathostomes, we can begin to understand the evolutionary history of the vertebrate genome. Specifically, the deep shared ancestry and rapid divergence of lampreys, hagfish and gnathostomes is considered evidence that the two versions of programmed rearrangement present in lamprey and hagfish (embryonic and immune receptor) were present in an ancestral lineage that existed more than 400 million years ago and perhaps included the ancestor of the jawed vertebrates. Validating this premise will require better characterization of the genome sequence and mechanisms of rearrangement in lamprey and hagfish.

Genome duplication and T cell immunity

The adaptive immune system (AIS) mediated by T cells and B cells arose ~450 million years ago in a common ancestor of jawed vertebrates. This system was so successful that, once established, it has been maintained in all classes of jawed vertebrates with only minor modifications. One event thought to have contributed to the emergence of this form of AIS is two rounds of whole-genome duplication. This event enabled jawed vertebrate ancestors to acquire many paralogous genes, known as ohnologs, with essential roles in T cell and B cell immunity. Ohnologs encode the key components of the antigen presentation machinery and signal transduction pathway for lymphocyte activation as well as numerous transcription factors important for lymphocyte development. Recently, it has been discovered that jawless vertebrates have developed an AIS employing antigen receptors unrelated to T/B cell receptors, but with marked overall similarities to the AIS of jawed vertebrates. Emerging evidence suggests that a common ancestor of all vertebrates was equipped with T-lymphoid and B-lymphoid lineages.