Unravelling the genomic landscape of divergence between lineages is key to understanding speciation. The naturally hybridizing collared flycatcher and pied are important avian speciation models that show pre- as well postzygotic isolation. We sequenced assembled 1.1-Gb genome, physically mapped assembly chromosomes using a low-density linkage map re-sequenced population samples each species. Here we species differentiation highly heterogeneous with approximately 50 'divergence islands'...

Abstract The typically repetitive nature of the sex-limited chromosome means that it is often excluded from or poorly covered in genome assemblies, hindering studies evolutionary and population genomic processes non-recombining chromosomes. Here, we present a draft assembly region collared flycatcher W chromosome, containing 46 genes without evidence female-specific functional differentiation. Survival during degeneration has been highly non-random expression data suggest this can be...

Significance Uniquely human biology is the result of genetic differences between humans and other primates, but identifying critical changes still poses a major challenge. We screened >32,000 human-specific substitutions in two classes putative transcriptional enhancers implicated evolution for their effects on enhancer activity neural stem cells, cell type fundamental cortical development expansion. identify hundreds that modify either alone or combination with variants. find different...

Changes in gene regulation have been linked to the expansion of human cerebral cortex and neurodevelopmental disorders, potentially by altering neural progenitor proliferation. However, effects genetic variation within regulatory elements on progenitors remain obscure. We use sgRNA-Cas9 screens stem cells (hNSCs) disrupt 10,674 genes 26,385 conserved regions 2,227 enhancers active developing determine Genes with proliferation phenotypes are associated disorders show biased expression...

Relatively little is known about the character of gene expression evolution as species diverge. It for instance unclear if generally evolves in a clock-like manner (by stabilizing selection or neutral evolution) there are frequent episodes directional selection. To gain insights into evolutionary divergence expression, we sequenced and compared transcriptomes multiple organs from population samples collared (Ficedula albicollis) pied flycatchers (F. hypoleuca), two which diverged less than...

Sex chromosome divergence, which follows the cessation of recombination and degeneration sex-limited chromosome, can cause a reduction in expression level for sex-linked genes heterozygous sex, unless some mechanisms dosage compensation develops to counter gene dose. Because large-scale perturbations levels arising from changes dose might have strong deleterious effects, evolutionary response should be strong. However, birds at least other female heterogametic organisms, wholesale sex does...

There is increasing evidence that dosage compensation not a ubiquitous feature following sex chromosome evolution, especially in organisms where females are the heterogametic sex, like birds. Even when it occurs, can be incomplete and limited to dosage-sensitive genes. However, previous work has mainly studied transcriptional regulation of sex-linked genes, which may reflect expression at protein level. Here, we used liquid chromatography-tandem mass spectrometry detect quantify expressed...

Abstract The molecular characteristics of the pseudoautosomal region (PAR) sex chromosomes remain elusive. Despite significant genome-sequencing efforts, PAR highly differentiated avian remains to be identified. Here we use linkage analysis together with whole-genome re-sequencing uncover 630-kb an ecological model species, collared flycatcher. contains 22 protein-coding genes and is GC rich. genetic length 64 cM in female meiosis, consistent obligate crossing-over event. Recombination...

Abstract The evolution of uniquely human traits likely entailed changes in developmental gene regulation. Human Accelerated Regions (HARs), which include transcriptional enhancers harboring a significant excess human-specific sequence changes, are leading candidates for driving regulatory modifications development. However, insight into whether HARs alter the level, distribution, and timing endogenous expression remains limited. We examined role HAR HACNS1 (HAR2) by interrogating its...

Abstract Background A detailed knowledge about spatial and temporal gene expression is important for understanding both the function of genes their evolution. For vast majority species, transcriptomes are still largely uncharacterized even in those where substantial information available it often form partially sequenced transcriptomes. With development next generation sequencing, a single experiment can now simultaneously identify transcribed part species genome estimate levels expression....

Genetic variants in the third intron of PRDM6 gene have been associated with BP traits multiple GWAS. By combining fine mapping, massively parallel reporter assays, and editing, we identified super enhancers that drive expression are partly regulated by STAT1 as causal for hypertension. The heterozygous disruption Prdm6 mice expressing Cre recombinase under control mouse smooth muscle cell protein 22-α promoter (Prdm6fl/+ SM22-Cre) exhibited a markedly higher number renin-producing cells...

Abstract Background Genetic changes that modify the function of transcriptional enhancers have been linked to evolution biological diversity across species. Multiple studies focused on role nucleotide substitutions, transposition, and insertions deletions in altering enhancer function. CpG islands (CGIs) recently shown influence activity, here we test how their turnover species contributes evolution. Results We integrate maps CGIs activity-associated histone modifications obtained from...

Abstract Human Accelerated Regions (HARs) are highly conserved across species but exhibit a significant excess of human-specific sequence changes, suggesting they may have gained novel functions in human evolution. HARs include transcriptional enhancers with activity and been implicated the evolution brain. However, our understanding how contributed to uniquely features brain is hindered by lack insight into genes pathways that regulate. It unclear whether acted altering expression gene...

Polymorphism in cis-regulatory sequences can lead to different levels of expression for the two alleles a gene, providing starting point evolution gene expression. Little is known about genome-wide abundance genetic variation regulation natural populations but analysis allele-specific (ASE) provides means investigating such variation. We performed RNA-seq multiple tissues from population samples closely related flycatcher species and developed Bayesian algorithm that maximizes data usage by...

Abstract Transcriptional enhancers orchestrate cell type- and time point-specific gene expression programs. Genetic variation within enhancer sequences is an important contributor to phenotypic including evolutionary adaptations human disease. Certain genes pathways may be more prone regulatory evolution than others, with different patterns across diverse organisms, but whether such exist has not been investigated at a sufficient scale. To address this question, we identified signatures of...

ABSTRACT Developmental gene expression patterns are orchestrated by thousands of distant-acting transcriptional enhancers. However, identifying enhancers essential for the their target genes has proven challenging. Maps long-range regulatory interactions may provide means to identify crucial developmental expression. To investigate this hypothesis, we used circular chromosome conformation capture coupled with interaction maps in mouse limb characterize topology Pitx1, which is hindlimb...

Abstract Sympatric speciation remains a central focus of evolutionary biology. Although some evidence shows occurring in this way, little is known about the gene expression evolution and characteristics population genetics as species diverge. Two closely related Gymnocypris fish (Gymnocypris chui scleracanthus), which come from small glacier lake Tibetan Plateau, Lake Langcuo, exist possible incipient sympatric adaptive ecological speciation. We generated large amounts RNA-Seq data multiple...

Abstract Genetic changes that altered the function of gene regulatory elements have been implicated in evolution human brain. However, identifying particular modified activity during neurodevelopment remains challenging. Here we used massively parallel enhancer assays neural stem cells to measure impact 32,776 human-specific substitutions on 1,363 Human Accelerated Regions (HARs) and 3,027 Gain Enhancers (HGEs), which include enhancers with novel activities humans. We found 31.9% active HARs...

Abstract Changes in gene regulation have been linked to the expansion of human cerebral cortex and neurodevelopmental disorders. However, biological effects genetic variation within developmental regulatory elements on corticogenesis are not well understood. We used sgRNA-Cas9 screens neural stem cells (hNSCs) disrupt 10,674 expressed genes 2,227 enhancers active developing determine resulting cellular proliferation. Gene disruptions affecting proliferation were enriched for associated with...

Abstract RNA-seq is a powerful tool for both discovery and experimentation. Most studies rely on library normalization to compare samples or reliably estimate quantitative gene expression levels. Over the years number of methods have been proposed. Review testing these provided evidence that commonly used perform well in simple tasks, but their performance challenging tasks has yet be evaluated. Here I test using two scenarios. My assessment reveals surprising shortcomings some identifies an...

Variation in gene expression is believed to make a significant contribution phenotypic diversity and divergence. The analysis of allele-specific (ASE) can reveal important insights into regulation. We developed novel method called RPASE (Read-backed Phasing-based ASE detection) test for genes that show ASE. With mapped RNA-seq data from single individual list SNPs the same as only input, capable aggregating information across multiple dependent producing individual-based gene-level tests...

Abstract Transcriptional enhancers orchestrate cell type- and time point-specific gene expression programs. Evolution of enhancer sequences can alter target without causing detrimental misexpression in other contexts. It has long been thought that this modularity allows evolutionary changes to escape pleiotropic constraints, which is especially important for constrained developmental patterning genes. However, there still little data supporting hypothesis. Here we identified signatures...

Abstract The evolution of uniquely human traits likely entailed changes in developmental gene regulation. Human Accelerated Regions (HARs), which include transcriptional enhancers harboring a significant excess human-specific sequence changes, are leading candidates for driving regulatory modifications development. However, insight into whether HARs alter the level, distribution and timing endogenous expression remains limited. We examined role HAR HACNS1 (HAR2) by interrogating its...