Primitive Duplicate Hox Clusters in the European Eel's Genome

The enigmatic life cycle and elongated body of the European eel (Anguilla anguilla L., 1758) have long motivated scientific enquiry. Recently, eel research has gained in urgency, as the population has dwindled to the point of critical endangerment. We have assembled a draft genome in order to facilitate advances in all provinces of eel biology. Here, we use the genome to investigate the eel's complement of the Hox developmental transcription factors. We show that unlike any other teleost fish, the eel retains fully populated, duplicate Hox clusters, which originated at the teleost-specific genome duplication. Using mRNA-sequencing and in situ hybridizations, we demonstrate that all copies are expressed in early embryos. Theories of vertebrate evolution predict that the retention of functional, duplicate Hox genes can give rise to additional developmental complexity, which is not immediately apparent in the adult. However, the key morphological innovation elsewhere in the eel's life history coincides with the evolutionary origin of its Hox repertoire

Hox cluster duplication in the basal teleost Hiodon alosoides (Osteoglossomorpha)

Large-scale—even genome-wide—duplications have repeatedly been invoked as an explanation for major radiations. Teleosts, the most species-rich vertebrate clade, underwent a “fish-specific genome duplication” (FSGD) that is shared by most ray-finned fish lineages. We investigate here the Hox complement of the goldeye (Hiodon alosoides), a representative of Osteoglossomorpha, the most basal teleostean clade. An extensive PCR survey reveals that goldeye has at least eight Hox clusters, indicating a duplicated genome compared to basal actinopterygians. The possession of duplicated Hox clusters is uncoupled to species richness. The Hox system of the goldeye is substantially different from that of other teleost lineages, having retained several duplicates of Hox genes for which crown teleosts have lost at least one copy. A detailed analysis of the PCR fragments as well as full length sequences of two HoxA13 paralogs, and HoxA10 and HoxC4 genes places the duplication event close in time to the divergence of Osteoglossomorpha and crown teleosts. The data are consistent with—but do not conclusively prove—that Osteoglossomorpha shares the FSGD

Major issues in the origins of ray‐finned fish ( A ctinopterygii) biodiversity

Ray‐finned fishes ( A ctinopterygii) dominate modern aquatic ecosystems and are represented by over 32000 extant species. The vast majority of living actinopterygians are teleosts; their success is often attributed to a genome duplication event or morphological novelties. The remainder are ‘living fossils’ belonging to a few depauperate lineages with long‐retained ecomorphologies: P olypteriformes (bichirs), H olostei (bowfin and gar) and C hondrostei (paddlefish and sturgeon). Despite over a century of systematic work, the circumstances surrounding the origins of these clades, as well as their basic interrelationships and diagnoses, have been largely mired in uncertainty. Here, I review the systematics and characteristics of these major ray‐finned fish clades, and the early fossil record of A ctinopterygii, in order to gauge the sources of doubt. Recent relaxed molecular clock studies have pushed the origins of actinopterygian crown clades to the mid‐late P alaeozoic [ S ilurian– C arboniferous; 420 to 298 million years ago ( M a)], despite a diagnostic body fossil record extending only to the later M esozoic (251 to 66 M a). This disjunct, recently termed the ‘ T eleost G ap’ (although it affects all crown lineages), is based partly on calibrations from potential P alaeozoic stem‐taxa and thus has been attributed to poor fossil sampling. Actinopterygian fossils of appropriate ages are usually abundant and well preserved, yet long‐term neglect of this record in both taxonomic and systematic studies has exacerbated the gaps and obscured potential synapomorphies. At the moment, it is possible that later P alaeozoic‐age teleost, holostean, chondrostean and/or polypteriform crown taxa sit unrecognized in museum drawers. However, it is equally likely that the ‘ T eleost G ap’ is an artifact of incorrect attributions to extant lineages, overwriting both a post‐ P alaeozoic crown actinopterygian radiation and the ecomorphological diversity of stem‐taxa.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/109271/1/brv12086.pd

Hox cluster intergenic sequence evolution

The Hox gene cluster system is highly conserved among jawed-vertebrates. Specifically, the coding region of Hox genes along with their spacing and occurrence is highly conserved throughout gnathostomes. The intergenic regions of these clusters however are more variable. During the construction of a comprehensive non-coding sequence database we discovered that the intergenic sequences appear to also be highly conserved among cartilaginous and lobe-finned fishes, but much more diverged and dynamic in the ray-finned fishes. Starting at the base of the Actinopterygii a turnover of otherwise highly conserved non-coding sequences begins. This turnover is extended well into the derived ray-finned fish clade, Teleostei. Evidence from our population genetic study suggests this turnover, which appears to be due mainly to loosened constraints at the macro-evolutionary level, is highlighted by evidence of strong positive selection acting at the micro-evolutionary level. During the construction of the non-coding sequence database we also discovered that along with evidence of both relaxed constraints and positive selection emerges a pattern of transposable elements found within the Hox gene cluster system. The highly conserved Chondrichthyes and Sacropterygii Hox gene clusters have an invasion of type I transposons whereas the Actinopterygii Hox gene clusters have an invasion of type II transposons. Specifically, the Tc1 transposon is found throughout the ray-finned fishes Hox gene clusters and is highlighted by the presence of two intact Tc1 transposons in and adjacent to bichir’s Hox gene clusters. Expression in human cell lines suggests that at least one of these Tc1 transposons are active. This combined with simulations ran in our lab point to transposons having a role in past and on-going restructuring of ray-finned fishes genomes. These findings help shed light on the possible genomic changes that occurred and are occurring within the ray-finned fish clade that help shed light on their past and present species radiations.Ph.D.Includes bibliographical referencesIncludes vitaby Jeremy Don Raincro

Phylogenetic analysis of mammalian SIP30 sequences indicating accelerated adaptation of functional domain in primates

SIP30, characterized by a coiled-coil functional domain, plays a key role in regulating synaptic vesicle exocytosis and is implicated in neuropathic pain resulting from peripheral nerve injury. Because neuropathic pain is studied in primates (including human), domesticated animals, and rodents, we conducted a phylogenetic analysis of SIP30 in selected species of these three groups of mammals. SIP30 exhibits a high degree of sequence divergence in comparison to its protein binding partners SNAP25 and ZW10, which show broad sequence conservation. Notably, we observed an increased rate of change in the highly conserved coiled-coil domain in the SIP30 protein, specifically within primates. This observation suggests an accelerated adaptation of this functional domain in primate species