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Abstract Background We describe the genome of the western painted turtle, Chrysemys picta bellii, one of the most widespread, abundant, and well-studied turtles. We place the genome into a comparative evolutionary context, and focus on genomic features associated with tooth loss, immune function, longevity, sex differentiation and determination, and the species' physiological capacities to withstand extreme anoxia and tissue freezing. Results Our phylogenetic analyses confirm that turtles are the sister group to living archosaurs, and demonstrate an extraordinarily slow rate of sequence evolution in the painted turtle. The ability of the painted turtle to withstand complete anoxia and partial freezing appears to be associated with common vertebrate gene networks, and we identify candidate genes for future functional analyses. Tooth loss shares a common pattern of pseudogenization and degradation of tooth-specific genes with birds, although the rate of accumulation of mutations is much slower in the painted turtle. Genes associated with sex differentiation generally reflect phylogeny rather than convergence in sex determination functionality. Among gene families that demonstrate exceptional expansions or show signatures of strong natural selection, immune function and musculoskeletal patterning genes are consistently over-represented. Conclusions Our comparative genomic analyses indicate that common vertebrate regulatory networks, some of which have analogs in human diseases, are often involved in the western painted turtle's extraordinary physiological capacities. As these regulatory pathways are analyzed at the functional level, the painted turtle may offer important insights into the management of a number of human health disorders.

In this study, we report evidence of a novel duplication of Melanocortin receptor 1 (Mc1r) in the cavefish genome. This locus was discovered following the observation of excessive allelic diversity in a ~820 bp fragment of Mc1r amplified via degenerate PCR from a natural population of Astyanax aeneus fish from Guerrero, Mexico. The cavefish genome reveals the presence of two closely related Mc1r open reading frames separated by a 1.46 kb intergenic region. One open reading frame corresponds to the previously reported Mc1r receptor, and the other open reading frame (duplicate copy) is 975 bp in length, encoding a receptor of 325 amino acids. Sequence similarity analyses position both copies in the syntenic region of the single Mc1r locus in 16 representative craniate genomes spanning bony fish (including Astyanax) to mammals, suggesting we discovered tandem duplicates of this important gene. The two Mc1r copies share ~89% sequence similarity and, within Astyanax, are more similar to one another compared to other melanocortin family members. Future studies will inform the precise functional significance of the duplicated Mc1r locus and if this novel copy number variant may have adaptive significance for the Astyanax lineage. Key words: cavefish, brown mutation, Guerrero, copy number variation. Dans ce travail, les auteurs rapportent des evidences pour une duplication inedite du recepteur 1 de la melanocortine (Mc1r) au sein du genome d'un poisson cavernicole. Ce locus a ete decouvert a la suite de l'observation d'une diversite allelique excessive au sein d'un fragment de ~820 pb de Mc1r amplifie au moyen d'amorces degenerees a partir d'une population naturelle de l'Astyanax aeneus provenant de Guerrero au Mexique. Le genome revele la presence de deux cadres de lectures Mc1r tres similaires separes l'un de l'autre par une region intergenique de 1,46 kb. Un cadre de lecture correspond au recepteur Mc1r rapporte anterieurement, tandis que l'autre cadre de lecture (copie dupliquee) mesure 975 pb et code pour un recepteur de 325 acides amines. Une analyse de similarite place les deux copies au sein de la region syntenique de l'unique locus Mc1r present chez 16 genomes representatifs des Craniata allant des poisson osseux (incluant l'Astyanax) jusqu'au mammiferes, ce qui suggere la decouverte d'un premier cas de duplication de ce gene important. Les deux copies de Mc1r sont similaires a ~89% et, au sein des Astyanax, sont plus semblables l'une a l'autre que les autres membres de la famille des melanocortines. De futures etudes pourront determiner l impact fonctionnel precis decoulant de la duplication du locus Mc1r et si ce variant de nombre de copies se veut adaptative au sein des Astyanax. [Traduit par la Redaction] Mots-cles: poisson cavernicoles, mutation brown, Guerrero, variation du nombre de copies., Introduction The gene melanocortin receptor 1 (Mc1r) encodes a seven-transmembrane domain G-protein coupled receptor expressed in melanin-producing cells (Tsatmali et al. 2002). This protein receptor binds [alpha]-melanophore stimulating hormone, resulting [...]

Recent colonization of extreme environments provides unique opportunities to study the early steps of adaptation and the potential for rapid convergent evolution. However, phenotypic shifts during recent colonization may also be due to plasticity in response to changes in the rearing environment. Here, we analyzed a suite of morphological and behavioral traits in paired surface, subterranean, and facultatively subterranean Mexican tetras (Astyanax mexicanus) from recent introductions in two separate watersheds outside of their native range. We found a variety of phenotypic and behavioral shifts between subterranean and surface populations that are similar to those observed in relatively ancient populations in Mexico. Despite this rapid morphological divergence, we found that most of these trait differences were due to plasticity in response to rearing environments. While most trait assays in common-garden, lab-raised fish indicated that phenotypic shifts in wild fish were the result of plasticity, we also found evidence of genetic control in several traits present in subterranean populations. Interestingly, wall following behavior, an important subterranean foraging behavior, was greater in lab-born subterranean fish than in lab-born surface fish, suggesting rapid divergence of this trait between subterranean and surface populations. Thus, this study sheds light on the early steps of subterranean evolution, identifies potential rapid behavioral evolution, and suggests that plasticity in traits involving exploratory behavior may facilitate subterranean colonization. [ABSTRACT FROM AUTHOR]