Investigating the role of the Melanocortin-1 Receptor gene in an extreme case of microgeographical variation in the pattern of melanin-based plumage pigmentation

Received: August 23, 2012; Accepted: October 26, 2012; Published: December 5, 2012The Réunion grey white-eye (Zosterops borbonicus) is a single-island endemic passerine bird that exhibits striking geographically structured melanic polymorphism at a very small spatial scale. We investigated the genetic basis of this color polymorphism by testing whether the melanocortin-1 receptor (MC1R), a gene often involved in natural melanic polymorphism in birds, was associated with the observed plumage variation. Although we found three non-synonymous mutations, we detected no association between MC1R variants and color morphs, and the main amino-acid variant found in the Réunion grey white-eye was also present at high frequency in the Mauritius grey white-eye (Zosterops mauritianus), its sister species which shows no melanic polymorphism. In addition, neutrality tests and analysis of population structure did not reveal any obvious pattern of positive or balancing selection acting on MC1R. Altogether these results indicate that MC1R does not play a role in explaining the melanic variation observed in the Réunion grey white-eye. We propose that other genes such as POMC, Agouti or any other genes involved in pigment synthesis will need to be investigated in future studies if we are to understand how selection shapes complex patterns of melanin-based plumage pigmentation.Peer reviewe

Defining the Effect of the 16p11.2 Duplication on Cognition, Behavior, and Medical Comorbidities

IMPORTANCE The 16p11.2 BP4-BP5 duplication is the copy number variant most frequently associated with autism spectrum disorder (ASD), schizophrenia, and comorbidities such as decreased body mass index (BMI). OBJECTIVES To characterize the effects of the 16p11.2 duplication on cognitive, behavioral, medical, and anthropometric traits and to understand the specificity of these effects by systematically comparing results in duplication carriers and reciprocal deletion carriers, who are also at risk for ASD. DESIGN, SETTING, AND PARTICIPANTS This international cohort study of 1006 study participants compared 270 duplication carriers with their 102 intrafamilial control individuals, 390 reciprocal deletion carriers, and 244 deletion controls from European and North American cohorts. Data were collected from August 1, 2010, to May 31, 2015 and analyzed from January 1 to August 14, 2015. Linear mixed models were used to estimate the effect of the duplication and deletion on clinical traits by comparison with noncarrier relatives. MAIN OUTCOMES AND MEASURES Findings on the Full-Scale IQ (FSIQ), Nonverbal IQ, and Verbal IQ; the presence of ASD or other DSM-IV diagnoses; BMI; head circumference; and medical data. RESULTS Among the 1006 study participants, the duplication was associated with a mean FSIQ score that was lower by 26.3 points between proband carriers and noncarrier relatives and a lower mean FSIQ score (16.2-11.4 points) in nonproband carriers. The mean overall effect of the deletion was similar (-22.1 points; P 100) compared with the deletion group (P < .001). Parental FSIQ predicted part of this variation (approximately 36.0% in hereditary probands). Although the frequency of ASD was similar in deletion and duplication proband carriers (16.0% and 20.0%, respectively), the FSIQ was significantly lower (by 26.3 points) in the duplication probands with ASD. There also were lower head circumference and BMI measurements among duplication carriers, which is consistent with the findings of previous studies. CONCLUSIONS AND RELEVANCE The mean effect of the duplication on cognition is similar to that of the reciprocal deletion, but the variance in the duplication is significantly higher, with severe and mild subgroups not observed with the deletion. These results suggest that additional genetic and familial factors contribute to this variability. Additional studies will be necessary to characterize the predictors of cognitive deficits

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

ABSTRACT: A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ∼1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.info:eu-repo/semantics/publishedVersio

Factors Associated with Revision Surgery after Internal Fixation of Hip Fractures

Background: Femoral neck fractures are associated with high rates of revision surgery after management with internal fixation. Using data from the Fixation using Alternative Implants for the Treatment of Hip fractures (FAITH) trial evaluating methods of internal fixation in patients with femoral neck fractures, we investigated associations between baseline and surgical factors and the need for revision surgery to promote healing, relieve pain, treat infection or improve function over 24 months postsurgery. Additionally, we investigated factors associated with (1) hardware removal and (2) implant exchange from cancellous screws (CS) or sliding hip screw (SHS) to total hip arthroplasty, hemiarthroplasty, or another internal fixation device. Methods: We identified 15 potential factors a priori that may be associated with revision surgery, 7 with hardware removal, and 14 with implant exchange. We used multivariable Cox proportional hazards analyses in our investigation. Results: Factors associated with increased risk of revision surgery included: female sex, [hazard ratio (HR) 1.79, 95% confidence interval (CI) 1.25-2.50; P = 0.001], higher body mass index (fo

Data from: First draft genome of an iconic clownfish species (Amphiprion frenatus)

Clownfishes (or anemonefishes) form an iconic group of coral reef fishes, principally known for their mutualistic interaction with sea anemones. They are characterized by particular life-history traits, such as a complex social structure and mating system involving sequential hermaphroditism, coupled with an exceptionally long lifespan. Additionally, clownfishes are considered to be one of the rare group to have experienced an adaptive radiation in the marine environment. Here, we assembled and annotated the first genome of a clownfish species, the tomato clownfish (Amphiprion frenatus). We obtained a total of 17,801 assembled scaffolds, containing a total of 26,917 genes. The completeness of the assembly and annotation was satisfying, with 96.5% of the Actinopterygii BUSCOs (benchmarking universal Single-Copy Orthologs) being retrieved in A. frenatus assembly. The quality of the resulting assembly is comparable to other bony fish assemblies. This resource is valuable for the advancing of studies of the particular life-history traits of clownfishes, as well as being useful for population genetic studies and the development of new phylogenetic markers. It will also open the way to comparative genomics. Indeed, future genomic comparison among closely related fishes may provide means to identify genes related to the unique adaptations to different sea anemone hosts, as well as better characterize the genomic signatures of an adaptive radiation

Timing and number of colonizations but not diversification rates affect diversity patterns in hemosporidian lineages on a remote oceanic archipelago

Parasite diversity on remote oceanic archipelagos is determined by the number and timing of colonizations and by in situ diversification rate. In this study, we compare intra-archipelago diversity of two hemosporidian parasite genera, Plasmodium and Leucocytozoon, infecting birds of the Mascarene archipelago. Despite the generally higher vagility of Plasmodium parasites, we report a diversity of Plasmodium cytochrome b haplotypes in the archipelago much lower than that of Leucocytozoon. Using phylogenetic data, we find that this difference in diversity is consistent with differences in the timing and number of colonizations, while rates of diversification do not vary significantly between the two genera. The prominence of immigration history in explaining current diversity patterns highlights the importance of historical contingencies in driving disparate biogeographic patterns in potentially harmful blood parasites infecting island birds

Holocene climate change promoted allopatric divergence and disjunct geographic distribution in a bee orchid species

International audienceAim: Species with disjunct geographic distributions provide natural opportunities to investigate incipient or recent allopatric divergence. The combination of both genetic and ecological data may be fruitful to decipher the causes of such pattern: i) actual vicariance, ii) successful colonization from one source range to a new range (dispersal, biological introduction) or iii) parallel convergent evolution. Location: Southern France and Northern Spain.Taxon: The bee orchid Ophrys aveyronensis (and its two recognized subspecies O. a. subsp. aveyronensis and O. a. subsp. vitorica) displays a disjunct geographic distribution with two subranges separated by 600 km on both sides of the Pyrenees mountain range. Methods As allopatric divergence is often complex to document in the wild, we used a combination of population genomics and Ecological Niche Modelling (ENM) to investigate the causes of this intriguing biogeographic pattern.Results:The population genomic data demonstrate that all the studied populations exhibit similar patterns of genetic diversity and dramatic decrease in effective size compared to the ancestral population. Significant genetic differentiation and reciprocal monophyly exist between populations of the two subranges of O. aveyronensis, despite a very recent divergence time as young as ca. 1500 generations ago. Moreover, (paleo-)ecological Niche Modelling analyses support that the disjunct geographic distribution of O. aveyronensis is consistent with a range split of a broad ancestral range, contraction and distinct longitudinal and latitudinal shifts in response to climate warming during the Holocene.Main Conclusion: The congruence of the results obtained from both population genomics and ENM approaches documents how very recent continental allopatric divergence initiated speciation in this system. Ophrys aveyronensis provides a promising opportunity to study the onset of reproductive isolation and parallel evolution following an initial stage of geographic separation in a group with high diversification rate

Characterization of the complete plastome of Delphinium montanum, a polyploid, endemic and endangered Pyrenean Larkspur

Delphinium montanum DC. 1815, is an endangered larkspur endemic to the Eastern Pyrenees. For biogeographic and conservation purpose, a hybrid assembly approach based on long- and short-read genomic data allowed us to successfully assemble whole plastid genome of Delphinium montanum. The complete plastome is 154,185 bp in length, consisting of a pair of inverted repeats (IRs) of 26,559 bp, a large single-copy (LSC) region and a small single-copy region (SSC) of 84,746 and 16,320 bp, respectively. It was found to contain 136 genes, including 84 protein-coding genes, 44 trRNA genes and 8 rRNA genes. The overall GC content of the plastid genome is 38.3%. Phylogenetic inference supports the polyphyly of the Delphinium genus

Data from: Timing and number of colonizations but not diversification rates affect diversity patterns in hemosporidian lineages on a remote oceanic archipelago

Parasite diversity on remote oceanic archipelagos is determined by the number and timing of colonizations, and in-situ diversification rate. In this study we compare intra-archipelago diversity of two hemosporidian parasite genera, Plasmodium and Leucocytozoon, infecting birds of the Mascarene archipelago. Despite the generally higher vagility of Plasmodium parasites, we report a much lower diversity of Plasmodium cytochrome-b haplotypes in the archipelago compared to Leucocytozoon. Using phylogenetic data, we find that this difference in diversity is consistent with differences in the timing and the number of colonizations, while rates of diversification do not vary significantly between the two genera. The prominence of immigration history in explaining current diversity patterns highlights the importance of historical contingencies in driving disparate biogeographic patterns in potentially harmful blood parasites infecting island birds