Conservation of shh cis-regulatory architecture of the coelacanth is consistent with its ancestral phylogenetic position

Early Mesozoic burst of morphological disparity in the slow-evolving coelacanth fish lineage

Since the split of the coelacanth lineage from other osteichthyans 420 million years ago, the morphological disparity of this clade has remained remarkably stable. Only few outliers with peculiar body shape stood out over the evolutionary history, but they were phylogenetically and stratigraphically independent of each other. Here, we report the discovery of a new clade of ancient latimeriid coelacanths representing a small flock of species present in the Western Tethys between 242 and 241 million years ago. Among the four species, two show highly derived anatomy. A new genus shows reversal to plesiomorphic conditions in its skull and caudal fin organisation. The new genus and its sister Foreyia have anatomical modules that moved from the general coelacanth Bauplau either in the same direction or in opposite direction that affect proportions of the body, opercle and fins. Comparisons with extant genetic models shows that changes of the regulatory network of the Hedgehog signal gene family may account for most of the altered anatomy. This unexpected, short and confined new clade represents the only known example of a burst of morphological disparity over the long history of coelacanths at a recovery period after the Permian-Triassic Mass Extinction.

A microanatomical and histological study of the scales of the Devonian sarcopterygian Miguashaia bureaui and the evolution of the squamation in coelacanths

Coelacanths have traditionally been described as morphologically conservative throughout their long evolutionary history, which spans more than 400 million years. After an initial burst during the Devonian, a morphological stasis was long thought to have prevailed since the Carboniferous, as shown by the extant Latimeria. New fossil discoveries have challenged this view, with punctual and sometimes unusual departures from the general coelacanth Bauplan. The dermal skeleton is considered to represent one, if not the main, example of morphological stasis in coelacanth evolution and as a consequence, has remained poorly surveyed. The lack of palaeohistological data on the dermoskeleton has resulted in a poor understanding of the early establishment and evolution of the coelacanth squamation. Here we describe the scales of Miguashaia bureaui from the Upper Devonian of Miguasha, Québec (Canada), revealing histological data for a Palaeozoic coelacanth in great detail and adding to our knowledge on the dermal skeleton of sarcopterygians. Miguashaia displays rounded scales ornamented by tubercules and narrow ridges made of dentine and capped with enamel. At least two generations of superimposed odontodes occur, which is reminiscent of the primitive condition of stem osteichthyans like Andreolepis or Lophosteus, and onychodonts like Selenodus. The middle vascular layer is well developed and shows traces of osteonal remodelling. The basal plate consists of a fully mineralised lamellar bone with a repetitive rotation pattern every five layers indicating a twisted plywood-like arrangement of the collagen plies. Comparisons with the extant Latimeria and other extinct taxa show that these features are consistently conserved across coelacanth evolution with only minute changes in certain taxa. The morphological and histological features displayed in the scales of Miguashaia enable us to draw a comprehensive picture of the onset of the coelacanth squamation and to propose and discuss evolutionary scenarios for the coelacanth dermoskeleton.

Gene regulatory landscape of the sonic hedgehog locus in embryonic development

The organs of vertebrate species display a wide variety of morphology. A remaining challenge in evolutionary developmental biology is to elucidate how vertebrate lineages acquire distinct morphological features. Developmental programs are driven by spatiotemporal regulation of gene expression controlled by hundreds of thousands of cis-regulatory elements. Changes in the regulatory elements caused by the introduction of genetic variants can confer regulatory innovation that may underlie morphological novelties. Recent advances in sequencing technology have revealed a number of potential regulatory variants that can alter gene expression patterns. However, a limited number of studies demonstrate causal dependence between genetic and morphological changes. Regulation of Shh expression is a good model to understand how multiple regulatory elements organize tissue-specific gene expression patterns. This model also provides insights into how evolution of molecular traits, such as gene regulatory networks, lead to phenotypic novelty.

Conserved Noncoding Elements in the Most Distant Genera of Cephalochordates: The Goldilocks Principle

Cephalochordates, the sister group of vertebrates + tunicates, are evolving particularly slowly. Therefore, genome comparisons between two congeners of Branchiostoma revealed so many conserved noncoding elements (CNEs), that it was not clear how many are functional regulatory elements. To more effectively identify CNEs with potential regulatory functions, we compared noncoding sequences of genomes of the most phylogenetically distant cephalochordate genera, Asymmetron and Branchiostoma, which diverged approximately 120-160 million years ago. We found 113,070 noncoding elements conserved between the two species, amounting to 3.3% of the genome. The genomic distribution, target gene ontology, and enriched motifs of these CNEs all suggest that many of them are probably cis-regulatory elements. More than 90% of previously verified amphioxus regulatory elements were re-captured in this study. A search of the cephalochordate CNEs around 50 developmental genes in several vertebrate genomes revealed eight CNEs conserved between cephalochordates and vertebrates, indicating sequence conservation over >500 million years of divergence. The function of five CNEs was tested in reporter assays in zebrafish, and one was also tested in amphioxus. All five CNEs proved to be tissue-specific enhancers. Taken together, these findings indicate that even though Branchiostoma and Asymmetron are distantly related, as they are evolving slowly, comparisons between them are likely optimal for identifying most of their tissue-specific cis-regulatory elements laying the foundation for functional characterizations and a better understanding of the evolution of developmental regulation in cephalochordates.

Identification and Validation of Novel Hedgehog-Responsive Enhancers Predicted by Computational Analysis of Ci/Gli Binding Site Density

The Hedgehog (Hh) signaling pathway directs a multitude of cellular responses during embryogenesis and adult tissue homeostasis. Stimulation of the pathway results in activation of Hh target genes by the transcription factor Ci/Gli, which binds to specific motifs in genomic enhancers. In Drosophila, only a few enhancers (patched, decapentaplegic, wingless, stripe, knot, hairy, orthodenticle) have been shown by in vivo functional assays to depend on direct Ci/Gli regulation. All but one (orthodenticle) contain more than one Ci/Gli site, prompting us to directly test whether homotypic clustering of Ci/Gli binding sites is sufficient to define a Hh-regulated enhancer. We therefore developed a computational algorithm to identify Ci/Gli clusters that are enriched over random expectation, within a given region of the genome. Candidate genomic regions containing Ci/Gli clusters were functionally tested in chicken neural tube electroporation assays and in transgenic flies. Of the 22 Ci/Gli clusters tested, seven novel enhancers (and the previously known patched enhancer) were identified as Hh-responsive and Ci/Gli-dependent in one or both of these assays, including: Cuticular protein 100A (Cpr100A); invected (inv), which encodes an engrailed-related transcription factor expressed at the anterior/posterior wing disc boundary; roadkill (rdx), the fly homolog of vertebrate Spop; the segment polarity gene gooseberry (gsb); and two previously untested regions of the Hh receptor-encoding patched (ptc) gene. We conclude that homotypic Ci/Gli clustering is not sufficient information to ensure Hh-responsiveness; however, it can provide a clue for enhancer recognition within putative Hedgehog target gene loci.

Divergent evolutionary rates in vertebrate and mammalian specific conserved non-coding elements (CNEs) in echolocating mammals

BACKGROUND

The majority of DNA contained within vertebrate genomes is non-coding, with a certain proportion of this thought to play regulatory roles during development. Conserved Non-coding Elements (CNEs) are an abundant group of putative regulatory sequences that are highly conserved across divergent groups and thus assumed to be under strong selective constraint. Many CNEs may contain regulatory factor binding sites, and their frequent spatial association with key developmental genes - such as those regulating sensory system development - suggests crucial roles in regulating gene expression and cellular patterning. Yet surprisingly little is known about the molecular evolution of CNEs across diverse mammalian taxa or their role in specific phenotypic adaptations. We examined 3,110 vertebrate-specific and ~82,000 mammalian-specific CNEs across 19 and 9 mammalian orders respectively, and tested for changes in the rate of evolution of CNEs located in the proximity of genes underlying the development or functioning of auditory systems. As we focused on CNEs putatively associated with genes underlying the development/functioning of auditory systems, we incorporated echolocating taxa in our dataset because of their highly specialised and derived auditory systems.

RESULTS

Phylogenetic reconstructions of concatenated CNEs broadly recovered accepted mammal relationships despite high levels of sequence conservation. We found that CNE substitution rates were highest in rodents and lowest in primates, consistent with previous findings. Comparisons of CNE substitution rates from several genomic regions containing genes linked to auditory system development and hearing revealed differences between echolocating and non-echolocating taxa. Wider taxonomic sampling of four CNEs associated with the homeobox genes Hmx2 and Hmx3 - which are required for inner ear development - revealed family-wise variation across diverse bat species. Specifically within one family of echolocating bats that utilise frequency-modulated echolocation calls varying widely in frequency and intensity high levels of sequence divergence were found.

CONCLUSIONS

Levels of selective constraint acting on CNEs differed both across genomic locations and taxa, with observed variation in substitution rates of CNEs among bat species. More work is needed to determine whether this variation can be linked to echolocation, and wider taxonomic sampling is necessary to fully document levels of conservation in CNEs across diverse taxa.

The structure and evolution of cis-regulatory regions: the shavenbaby story

In this paper, we provide a historical account of the contribution of a single line of research to our current understanding of the structure of cis-regulatory regions and the genetic basis for morphological evolution. We revisit the experiments that shed light on the evolution of larval cuticular patterns within the genus Drosophila and the evolution and structure of the shavenbaby gene. We describe the experiments that led to the discovery that multiple genetic changes in the cis-regulatory region of shavenbaby caused the loss of dorsal cuticular hairs (quaternary trichomes) in first instar larvae of Drosophila sechellia. We also discuss the experiments that showed that the convergent loss of quaternary trichomes in D. sechellia and Drosophila ezoana was generated by parallel genetic changes in orthologous enhancers of shavenbaby. We discuss the observation that multiple shavenbaby enhancers drive overlapping patterns of expression in the embryo and that these apparently redundant enhancers ensure robust shavenbaby expression and trichome morphogenesis under stressful conditions. All together, these data, collected over 13 years, provide a fundamental case study in the fields of gene regulation and morphological evolution, and highlight the importance of prolonged, detailed studies of single genes.

Single-male paternity in coelacanths

Latimeria chalumnae, a 'living fossil,' is of great scientific interest, as it is closely related to the aquatic ancestors of land-living tetrapods. Latimeria show internal fertilization and bear live young, but their reproductive behaviour is poorly known. Here we present for the first time a paternity analysis of the only available material from gravid females and their offspring. We genotype two L. chalumnae females and their unborn brood for 14 microsatellite loci. We find that the embryos are closely related to each other and never show more than three different alleles per locus, providing evidence for a single father siring all of the offspring. We reconstruct the father's genotype but cannot identify it in the population. These data suggest that coelacanths have a monogamous mating system and that individual relatedness is not important for mate choice.

Comparative genomics of the Hedgehog loci in chordates and the origins of Shh regulatory novelties

The origin and evolution of the complex regulatory landscapes of some vertebrate developmental genes, often spanning hundreds of Kbp and including neighboring genes, remain poorly understood. The Sonic Hedgehog (Shh) genomic regulatory block (GRB) is one of the best functionally characterized examples, with several discrete enhancers reported within its introns, vast upstream gene-free region and neighboring genes (Lmbr1 and Rnf32). To investigate the origin and evolution of this GRB, we sequenced and characterized the Hedgehog (Hh) loci from three invertebrate chordate amphioxus species, which share several early expression domains with Shh. Using phylogenetic footprinting within and between chordate lineages, and reporter assays in zebrafish probing >30 Kbp of amphioxus Hh, we report large sequence and functional divergence between both groups. In addition, we show that the linkage of Shh to Lmbr1 and Rnf32, necessary for the unique gnatostomate-specific Shh limb expression, is a vertebrate novelty occurred between the two whole-genome duplications.

Genome size, GC percentage and 5mC level in the Indonesian coelacanth Latimeria menadoensis

The living fossil Latimeria menadoensis is important to understand sarcopterygian evolution. To gain further insights into this fish species we studied its genome size, GC% and 5mC level. The genome size and the GC% of the Indonesian coelacanth seem to be very similar to those of the African coelacanth. Moreover the GC%, the CpG frequency and the 5mC level of L. menadoensis are more similar to those of fish and amphibians than to those of mammals, birds and reptiles and this is in line with the hypothesis that two different DNA methylation and CpG shortage equilibria arose during vertebrate evolution. Our results suggest that the genome of L. menadoensis has remained unchanged for several million years, maybe since the origin of the lineage which from lobe-finned fish led to tetrapods. These data fit a conservative evolutionary landscape and suggest that the genome of the extant crossopterygians may be a sort of evolutionarily frozen genome.

Two lamprey Hedgehog genes share non-coding regulatory sequences and expression patterns with gnathostome Hedgehogs

Hedgehog (Hh) genes play major roles in animal development and studies of their evolution, expression and function point to major differences among chordates. Here we focused on Hh genes in lampreys in order to characterize the evolution of Hh signalling at the emergence of vertebrates. Screening of a cosmid library of the river lamprey Lampetra fluviatilis and searching the preliminary genome assembly of the sea lamprey Petromyzon marinus indicate that lampreys have two Hh genes, named Hha and Hhb. Phylogenetic analyses suggest that Hha and Hhb are lamprey-specific paralogs closely related to Sonic/Indian Hh genes. Expression analysis indicates that Hha and Hhb are expressed in a Sonic Hh-like pattern. The two transcripts are expressed in largely overlapping but not identical domains in the lamprey embryonic brain, including a newly-described expression domain in the nasohypophyseal placode. Global alignments of genomic sequences and local alignment with known gnathostome regulatory motifs show that lamprey Hhs share conserved non-coding elements (CNE) with gnathostome Hhs albeit with sequences that have significantly diverged and dispersed. Functional assays using zebrafish embryos demonstrate gnathostome-like midline enhancer activity for CNEs contained in intron2. We conclude that lamprey Hh genes are gnathostome Shh-like in terms of expression and regulation. In addition, they show some lamprey-specific features, including duplication and structural (but not functional) changes in the intronic/regulatory sequences.