How structural variants shape avian phenotypes: Lessons from model systems.

Despite receiving significant recent attention, the relevance of structural variation (SV) in driving phenotypic diversity remains understudied, although recent advances in long-read sequencing, bioinformatics and pangenomic approaches have enhanced SV detection. We review the role of SVs in shaping phenotypes in avian model systems, and identify some general patterns in SV type, length and their associated traits. We found that most of the avian SVs so far identified are short indels in chickens, which are frequently associated with changes in body weight and plumage colouration. Overall, we found that relatively short SVs are more frequently detected, likely due to a combination of their prevalence compared to large SVs, and a detection bias, stemming primarily from the widespread use of short-read sequencing and associated analytical methods. SVs most commonly involve non-coding regions, especially introns, and when patterns of inheritance were reported, SVs associated primarily with dominant discrete traits. We summarise several examples of phenotypic convergence across different species, mediated by different SVs in the same or different genes and different types of changes in the same gene that can lead to various phenotypes. Complex rearrangements and supergenes, which can simultaneously affect and link several genes, tend to have pleiotropic phenotypic effects. Additionally, SVs commonly co-occur with single-nucleotide polymorphisms, highlighting the need to consider all types of genetic changes to understand the basis of phenotypic traits. We end by summarising expectations for when long-read technologies become commonly implemented in non-model birds, likely leading to an increase in SV discovery and characterisation. The growing interest in this subject suggests an increase in our understanding of the phenotypic effects of SVs in upcoming years.

Adaptive phenotypic and genomic divergence in the common chaffinch (Fringilla coelebs) following niche expansion within a small oceanic island.

According to models of ecological speciation, adaptation to adjacent, contrasting habitat types can lead to population divergence given strong enough environment-driven selection to counteract the homogenizing effect of gene flow. We tested this hypothesis in the common chaffinch (Fringilla coelebs) on the small island of La Palma, Canary Islands, where it occupies two markedly different habitats. Isotopic (δ13 C, δ15 N) analysis of feathers indicated that birds in the two habitats differed in ecosystem and/or diet, and analysis of phenotypic traits revealed significant differences in morphology and plumage colouration that are consistent with ecomorphological and ecogeographical predictions respectively. A genome-wide survey of single-nucleotide polymorphism revealed marked neutral structure that was consistent with geography and isolation by distance, suggesting low dispersal. In contrast, loci putatively under selection identified through genome-wide association and genotype-environment association analyses, revealed amarked adaptive divergence between birds in both habitats. Loci associated with phenotypic and environmental differences among habitats were distributed across the genome, as expected for polygenic traits involved in local adaptation. Our results suggest a strong role for habitat-driven local adaptation in population divergence in the chaffinches of La Palma, a process that appears to be facilitated by a strong reduction in effective dispersal distances despite the birds' high dispersal capacity.

Sequential colonization of oceanic archipelagos led to a species-level radiation in the common chaffinch complex (Aves: Fringilla coelebs).

Oceanic archipelagos are excellent systems for studying speciation, yet inference of evolutionary process requires that the colonization history of island organisms be known with accuracy. Here, we used phylogenomics and patterns of genetic diversity to infer the sequence and timing of colonization of Macaronesia by mainland common chaffinches (Fringilla coelebs), and assessed whether colonization of the different archipelagos has resulted in a species-level radiation. To reconstruct the evolutionary history of the complex we generated a molecular phylogeny based on genome-wide SNP loci obtained from genotyping-by-sequencing, we ran ancestral range biogeographic analyses, and assessed fine-scale genetic structure between and within archipelagos using admixture analysis. To test for a species-level radiation, we applied a probabilistic tree-based species delimitation method (mPTP) and an integrative taxonomy approach including phenotypic differences. Results revealed a circuitous colonization pathway in Macaronesia, from the mainland to the Azores, followed by Madeira, and finally the Canary Islands. The Azores showed surprisingly high genetic diversity, similar to that found on the mainland, and the other archipelagos showed the expected sequential loss of genetic diversity. Species delimitation methods supported the existence of several species within the complex. We conclude that the common chaffinch underwent a rapid radiation across Macaronesia that was driven by the sequential colonization of the different archipelagos, resulting in phenotypically and genetically distinct, independent evolutionary lineages. We recommend a taxonomic revision of the complex that takes into account its genetic and phenotypic diversity.

Relationship between childhood trauma, mindfulness, and dissociation in subjects with and without hallucination proneness.

The purpose of this study was to examine the relationship between childhood traumas, mindfulness, and dissociation (more specifically, absorption and depersonalization) in healthy subjects with and without hallucination proneness. A sample of 318 subjects was given the Launay-Slade Hallucination Scale-Revised (R. P. Bentall & P. Slade, 1985). From this sample, 2 groups were formed: one with high and the other with low hallucination proneness. Furthermore, all participants were given the Tellegen Absorption Scale (A. Tellegen & G. Atkinson, 1974), the Cambridge Depersonalization Scale (M. Sierra & G. E. Berrios, 2000), the Southampton Mindfulness Questionnaire (P. D. J. Chadwick et al., 2008), and the Trauma Questionnaire (J. R. E. Davidson, D. Hughes, & D. G. Blazer, 1990). The results showed that in the group with high hallucination proneness, there were significantly more subjects with traumatic experiences than in the group with low predisposition, although no significant difference in the mean number of traumatic experiences undergone in childhood was found between the 2 groups, although there was a trend toward significance. A correlation analysis showed a significant negative association between mindfulness on the one hand and absorption and depersonalization on the other. A positive relationship was also found between childhood traumas and absorption and depersonalization. Finally, multiple mediation analysis showed that the absorption and depersonalization variables acted as mediators between childhood traumas and hallucination proneness. We discuss the importance of the relationship between the variables studied and hallucination proneness and suggest some approaches for their treatment.

Relationship of absorption, depersonalisation, and self-focused attention in subjects with and without hallucination proneness.

INTRODUCTION: The purpose of this work was to study the relationship of absorption, depersonalisation, and self-focused attention in subjects prone to hallucination. METHODS: A sample of 218 healthy subjects was given the LSHS-R Hallucination Scale (Bentall & Slade, 1985). Three groups, subjects with high, medium, and low hallucination proneness, were formed from this sample. The Tellegen Absorption Scale (TAS; Tellegen & Atkinson, 1974), Cambridge Depersonalisation Scale (CDS; Sierra & Berrios, 2000), and Self-Absorption Scale (SAS; McKenzie & Hoyle, 2008) were also given to all the participants. The Metacognitions Questionnaire (MCQ-30; Wells & Cartwright-Hatton, 2004) was used as a covariant to control for the effects of emotional vulnerability on the dependent variables studied. RESULTS: The results showed that subjects highly prone to hallucinations had significantly higher absorption, depersonalisation, and self-focused attention than the subjects in the other two groups. A hierarchical regression analysis showed that absorption and depersonalisation predict hallucination proneness. CONCLUSIONS: The importance of the absorption, depersonalisation, and self-focused attention variables for understanding the aetiology of hallucinations is discussed in the Conclusions, where some approaches to its treatment are also suggested.

Dissociative experiences as mediators between childhood trauma and auditory hallucinations.

The purpose of this work was to study the relationship between reported traumatic experiences in childhood and positive psychotic symptoms. We hypothesized that dissociative experiences were potential mediators between childhood trauma and hallucinations, but not delusions. The sample comprised 71 patients diagnosed with psychoses. They were assessed with the Dissociative Experiences Scale (DES-II; Carlson & Putnam, 1993), a questionnaire on trauma (TQ; Davidson, Hughes, & Blazer, 1990), and the Positive and Negative Syndrome Scale (PANSS; Kay, Opler, & Lindenmayer, 1988) delusions and hallucinations items. The results showed that childhood trauma was positively associated with the dissociation scale scores (r = .40) and also the hallucination (r = .36) and delusions scale scores (r = .32). Furthermore, it was demonstrated that the dissociation variable was a potential mediator between childhood trauma and hallucinations, but not between childhood trauma and delusions. Of the 3 DES-II factors, only depersonalization showed a mediating relationship between childhood trauma and hallucinations. The main conclusion is that the impact of childhood trauma on hallucinations may not simply be direct, but mediated by dissociative experiences, especially depersonalization. Clinical implications are also briefly discussed.

Relationship of metacognition, absorption, and depersonalization in patients with auditory hallucinations.

OBJECTIVES: The purpose of this work was to study the relationship of metacognition, absorption, and depersonalization in hallucinating patients. DESIGN: A within-subjects correlational design was employed. METHODS: We formed four groups from a clinical population (schizophrenic patients with hallucinations, schizophrenic patients with no hallucinations but with delusions, schizophrenic patients recovered from positive symptoms, and patients with a non-psychotic psychiatric disorder) and a non-clinical control group. All participants were given the Metacognitions Questionnaire (MCQ-30, Wells & Cartwright-Hatton, 2004), the Tellegen Absorption Scale (TAS, Tellegen & Atkinson, 1974) and the Cambridge Depersonalization Scale (CDS, Sierra & Berrios, 2000). RESULTS: Schizophrenic subjects with hallucinations scored significantly higher on the depersonalization scale than any other group, and significantly higher on the absorption scale than any group except for the clinical patient controls. Schizophrenic patients with hallucinations also had significantly more dysfunctional metacognitive beliefs than subjects with no psychiatric pathology. It was further found that the metacognition variable correlated positively with the absorption and depersonalization variables, and that these variables in turn correlated positively with each other. Finally, it should be stressed that the variables that best predict hallucination severity are depersonalization and the MCQ-30 subscale `Need to control thoughts'. CONCLUSIONS: We discuss the role of metacognitive and dissociative variables in understanding hallucinations and suggest some approaches to their treatment.

Depersonalization as a mediator in the relationship between self-focused attention and auditory hallucinations.

The purpose of this work was to study the potentially mediating role of certain dissociative factors, such as depersonalization, between self-focused attention and auditory hallucinations. A total of 59 patients diagnosed with schizophrenic disorder completed a self-focused attention scale ( M. F. Scheier & C. S. Carver, 1985 ), the Cambridge Depersonalization Scale (M. Sierra & G. E. Berrios, 2000), and the hallucination and delusion items on the Positive and Negative Syndrome Scale (S. R. Kay, L. A. Opler, & J. P. Lindenmayer, 1988). The results showed that self-focused attention correlated positively with auditory hallucinations, with delusions, and with depersonalization. It was also demonstrated that depersonalization has a mediating role between self-focused attention and auditory hallucinations but not delusions. In the discussion, the importance of dissociative processes in understanding the formation and maintenance of auditory hallucinations is suggested.

Chromosome-Level Genome Assembly of the Common Chaffinch (Aves: Fringilla coelebs): A Valuable Resource for Evolutionary Biology.

The common chaffinch, Fringilla coelebs, is one of the most common, widespread, and well-studied passerines in Europe, with a broad distribution encompassing Western Europe and parts of Asia, North Africa, and the Macaronesian archipelagos. We present a high-quality genome assembly of the common chaffinch generated using Illumina shotgun sequencing in combination with Chicago and Hi-C libraries. The final genome is a 994.87-Mb chromosome-level assembly, with 98% of the sequence data located in chromosome scaffolds and a N50 statistic of 69.73 Mb. Our genome assembly shows high completeness, with a complete BUSCO score of 93.9% using the avian data set. Around 7.8% of the genome contains interspersed repetitive elements. The structural annotation yielded 17,703 genes, 86.5% of which have a functional annotation, including 7,827 complete universal single-copy orthologs out of 8,338 genes represented in the BUSCO avian data set. This new annotated genome assembly will be a valuable resource as a reference for comparative and population genomic analyses of passerine, avian, and vertebrate evolution.

Island songbirds as windows into evolution in small populations.

Due to their limited ranges and inherent isolation, island species have long been recognized as crucial systems for tackling a range of evolutionary questions, including in the early study of speciation.1,2 Such species have been less studied in the understanding of the evolutionary forces driving DNA sequence evolution. Island species usually have lower census population sizes (N) than continental species and, supposedly, lower effective population sizes (Ne). Given that both the rates of change caused by genetic drift and by selection are dependent upon Ne, island species are theoretically expected to exhibit (1) lower genetic diversity, (2) less effective natural selection against slightly deleterious mutations,3,4 and (3) a lower rate of adaptive evolution.5-8 Here, we have used a large set of newly sequenced and published whole-genome sequences of Passerida species (14 insular and 11 continental) to test these predictions. We confirm that island species exhibit lower census size and Ne, supporting the hypothesis that the smaller area available on islands constrains the upper bound of Ne. In the insular species, we find lower nucleotide diversity in coding regions, higher ratios of non-synonymous to synonymous polymorphisms, and lower adaptive substitution rates. Our results provide robust evidence that the lower Ne experienced by island species has affected both the ability of natural selection to efficiently remove weakly deleterious mutations and also the adaptive potential of island species, therefore providing considerable empirical support for the nearly neutral theory. We discuss the implications for both evolutionary and conservation biology.

A preliminary exploration of trauma, dissociation, and positive psychotic symptoms in a Spanish sample.

The purpose of this research was to study traumatic and dissociative experiences in a sample of Spanish psychotic patients. A total of 37 psychotic patients filled out the Dissociative Experiences Scale (E. B. Carlson & F. W. Putnam, 1993), a questionnaire on traumas (J. R. E. Davidson, D. Hughes, & D. G. Blazer, 1990), and the Positive and Negative Syndrome Scale delusion and hallucinations items (S. R. Kay, L. A. Opler, & J. P. Lindenmayer, 1988). The results showed that 40.5% of the subjects in the sample had undergone at least 1 traumatic experience as children and 64.9% had as adults. Patients with hallucinations had experienced a higher mean number of childhood traumatic experiences than patients without hallucinations. No significant difference in the mean number of traumatic events was found between patients with and without delusions. There was no significant difference in the mean number of adulthood traumatic events between patients with and without hallucinations and delusions. Subjects with childhood traumas scored higher on the Dissociative Experiences Scale than those who had had such experiences as adults. Patients with hallucinations and delusions also scored higher on the dissociation scale than patients who did not show those positive psychotic symptoms.

Relationship between self-focused attention and dissociation in patients with and without auditory hallucinations.

The purpose of this work was to study the relationship between self-focused attention and dissociative experiences in 4 groups of subjects: patients with a psychotic disorder who suffer from auditory hallucinations, patients with psychoses who have recovered from their hallucinations, patients with psychoses who have never had them, and a fourth nonclinical group. The private self-consciousness scale, revised version by Scheier and Carver, J Appl Soc Psychol. 1985;15:687-699, was used to measure self-focused attention, and the dissociative experience scale (DES-II, Bernstein and Putnam, J Nerv Ment Dis. 1986;174:727-735) was used for dissociation. The results showed that the attention of subjects with hallucinations was more self-focused than the nonclinical group, but did not differentiate significantly from groups of patients without hallucinations. On the other hand, patients with hallucinations and those recovered from them had a higher percentage of dissociative experiences than the rest of the groups in the total DES-II score and in its 3 factors, dissociative amnesia, depersonalization, and absorption. We also found a positive correlation between self-focusing and dissociative experiences in subjects with hallucinations. The depersonalization factor on the DES-II was the only factor predicting auditory hallucinations. The conclusions discuss the relevance of dissociative factors and self-focused attention to understanding the etiology of auditory hallucinations and their contributions to current cognitive models of hallucinations.

Relationship between self-focused attention and mindfulness in people with and without hallucination proneness.

The purpose of this work was to study the relationship between self-focused attention and mindfulness in participants prone to hallucinations and others who were not. A sample of 318 healthy participants, students at the universities of Sevilla and Almería, was given the Launay-Slade Hallucinations Scale-revised (LSHS-R, Bentall & Slade, 1985). Based on this sample, two groups were formed: participants with high (n = 55) and low proneness (n = 28) to hallucinations. Participants with a score higher than a standard deviation from the mean in the LSHS-R were included in the high proneness group, participants with a score lower than a standard deviation from the mean in the LSHR-R were included in the second one. All participants were also given the Self-Absorption Scale (SAS, McKenzie & Hoyle, 2008) and the Southampton Mindfulness Questionnaire (SMQ, Chadwick et al., 2008). The results showed that participants with high hallucination proneness had significantly higher levels of public (t(80) = 6.81, p < .001) and private (t(77) = 7.39, p < .001) self-focused attention and lower levels of mindfulness (t(81) = -4.56, p < .001) than participants in the group with low hallucination proneness. A correlational analysis showed a negative association between self-focused attention (private and public) and mindfulness (r = -0.23, p < .001; r = -0.38, p < .001 respectively). Finally, mindfulness was found to partly mediate between self-focused attention and hallucination proneness. The importance of self-focused attention and mindfulness in understanding the etiology of hallucinations discussed and suggest some approaches to their treatment.