Selection on a pleiotropic color gene block underpins early differentiation between two warbler species

AbstractWhen one species gradually splits into two, divergent selection on specific traits can cause peaks of differentiation in the genomic regions encoding those traits. Whether speciation is initiated by strong selection on a few genomic regions with large effects or by more diffused selection on many regions with small effects remains controversial. Differentiated phenotypes between differentiating lineages are commonly involved in reproductive isolation, thus their genetic underpinnings are key to the genomics architecture of speciation. When two species hybridize, recombination over multiple generations can help reveal the genetic regions responsible for the differentiated phenotypes against a genomic background that has been homogenized via backcrossing and introgression. We used admixture mapping to investigate genomic differentiation and the genetic basis of differentiated plumage features (relative melanin and carotenoid pigment) between hybridizing sister species in the early stage of speciation: Townsend’s (Setophaga townsendi) and Hermit warblers (S. occidentalis). We found a few narrow and dispersed divergent regions between allopatric parental populations, consistent with the ‘divergence with gene flow’ model of speciation. One of the divergent peaks involves three genes known to affect pigmentation: ASIP, EIF2S2, and RALY (the ASIP-RALY gene block). After controlling for population substructure, we found that a single nucleotide polymorphism (SNP) inside the intron of RALY displays a strong pleiotropic association with cheek, crown, and breast coloration. In addition, we detect selection on the ASIP-RALY gene block, as the geographic cline of the RALY marker of this gene block has remained narrower than the plumage cline, which remained narrower than expected under neutral diffusion over two decades. Despite extensive gene flow between these species across much of the genome, the selection on ASIP-RALY gene block maintains stable genotypic and plumage difference between species allowing further differentiation to accumulate via linkage to its flanking genetic region or linkage-disequilibrium genome-wide.

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Candidate Genes for the High-Altitude Adaptations of Two Mountain Pine Taxa

International Journal of Molecular Sciences ◽

10.3390/ijms22073477 ◽

2021 ◽

Vol 22 (7) ◽

pp. 3477

Author(s):

Julia Zaborowska ◽

Bartosz Łabiszak ◽

Annika Perry ◽

Stephen Cavers ◽

Witold Wachowiak

Keyword(s):

Population Structure ◽

Candidate Genes ◽

Genetic Basis ◽

Redox Homeostasis ◽

Snp Markers ◽

Regulation Of Transcription ◽

Single Nucleotide ◽

Homeostasis Regulation ◽

Genomic Regions ◽

Mountain Plants

Mountain plants, challenged by vegetation time contractions and dynamic changes in environmental conditions, developed adaptations that help them to balance their growth, reproduction, survival, and regeneration. However, knowledge regarding the genetic basis of species adaptation to higher altitudes remain scarce for most plant species. Here, we attempted to identify such corresponding genomic regions of high evolutionary importance in two closely related European pines, Pinus mugo and P. uncinata, contrasting them with a reference lowland relative—P. sylvestris. We genotyped 438 samples at thousands of single nucleotide polymorphism (SNP) markers, tested their genetic differentiation and population structure followed by outlier detection and gene ontology annotations. Markers clearly differentiated the species and uncovered patterns of population structure in two of them. In P. uncinata three Pyrenean sites were grouped together, while two outlying populations constituted a separate cluster. In P. sylvestris, Spanish population appeared distinct from the remaining four European sites. Between mountain pines and the reference species, 35 candidate genes for altitude-dependent selection were identified, including such encoding proteins responsible for photosynthesis, photorespiration and cell redox homeostasis, regulation of transcription, and mRNA processing. In comparison between two mountain pines, 75 outlier SNPs were found in proteins involved mainly in the gene expression and metabolism.

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Behavior-dependent cis regulation reveals genes and pathways associated with bower building in cichlid fishes

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1810140115 ◽

2018 ◽

Vol 115 (47) ◽

pp. E11081-E11090 ◽

Cited By ~ 15

Author(s):

Ryan A. York ◽

Chinar Patil ◽

Kawther Abdilleh ◽

Zachary V. Johnson ◽

Matthew A. Conte ◽

...

Keyword(s):

Gene Expression ◽

Neural Plasticity ◽

Genetic Basis ◽

Specific Expression ◽

Preferential Expression ◽

Cichlid Fishes ◽

Brain Gene Expression ◽

Genome Wide ◽

Allele Specific ◽

Genomic Regions

Many behaviors are associated with heritable genetic variation [Kendler and Greenspan (2006) Am J Psychiatry 163:1683–1694]. Genetic mapping has revealed genomic regions or, in a few cases, specific genes explaining part of this variation [Bendesky and Bargmann (2011) Nat Rev Gen 12:809–820]. However, the genetic basis of behavioral evolution remains unclear. Here we investigate the evolution of an innate extended phenotype, bower building, among cichlid fishes of Lake Malawi. Males build bowers of two types, pits or castles, to attract females for mating. We performed comparative genome-wide analyses of 20 bower-building species and found that these phenotypes have evolved multiple times with thousands of genetic variants strongly associated with this behavior, suggesting a polygenic architecture. Remarkably, F1 hybrids of a pit-digging and a castle-building species perform sequential construction of first a pit and then a castle bower. Analysis of brain gene expression in these hybrids showed that genes near behavior-associated variants display behavior-dependent allele-specific expression with preferential expression of the pit-digging species allele during pit digging and of the castle-building species allele during castle building. These genes are highly enriched for functions related to neurodevelopment and neural plasticity. Our results suggest that natural behaviors are associated with complex genetic architectures that alter behavior via cis-regulatory differences whose effects on gene expression are specific to the behavior itself.

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Emerging Technologies for Genome-Wide Profiling of DNA Breakage

Frontiers in Genetics ◽

10.3389/fgene.2020.610386 ◽

2021 ◽

Vol 11 ◽

Author(s):

Matthew J. Rybin ◽

Melina Ramic ◽

Natalie R. Ricciardi ◽

Philipp Kapranov ◽

Claes Wahlestedt ◽

...

Keyword(s):

Genome Instability ◽

Dna Double Strand Breaks ◽

Single Nucleotide ◽

Strand Breaks ◽

Single Strand Breaks ◽

Genome Wide ◽

A Genome ◽

Wide Scale ◽

Nucleotide Resolution ◽

Genomic Regions

Genome instability is associated with myriad human diseases and is a well-known feature of both cancer and neurodegenerative disease. Until recently, the ability to assess DNA damage—the principal driver of genome instability—was limited to relatively imprecise methods or restricted to studying predefined genomic regions. Recently, new techniques for detecting DNA double strand breaks (DSBs) and single strand breaks (SSBs) with next-generation sequencing on a genome-wide scale with single nucleotide resolution have emerged. With these new tools, efforts are underway to define the “breakome” in normal aging and disease. Here, we compare the relative strengths and weaknesses of these technologies and their potential application to studying neurodegenerative diseases.

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Genetic architecture and heritability of early-life telomere length in a wild passerine

10.22541/au.161961744.48479988/v1 ◽

2021 ◽

Author(s):

Michael Pepke ◽

Thomas Kvalnes ◽

Sarah Lundregan ◽

Winnie Boner ◽

Pat Monaghan ◽

...

Keyword(s):

Body Size ◽

Telomere Length ◽

Early Life ◽

Genetic Basis ◽

Skeletal Development ◽

Cellular Growth ◽

Phenotypic Correlation ◽

Animal Populations ◽

Genome Wide ◽

Genomic Regions

Early-life telomere length (TL) is associated with fitness in a range of organisms. Little is known about the genetic basis of variation in TL in wild animal populations, but to understand the evolutionary and ecological significance of TL it is important to quantify the relative importance of genetic and environmental variation in TL. In this study, we measured TL in 2746 house sparrow nestlings sampled across 20 years and used an animal model to show that there is a small heritable component of early-life TL (h2=0.04), but with a strong component of maternal inheritance. Variation in TL among individuals was mainly driven by environmental (year) variance, but also brood and parental effects. We did not find evidence for a negative genetic correlation underlying the observed negative phenotypic correlation between TL and structural body size. Thus, TL may evolve independently of body size and the negative phenotypic correlation is likely to be caused by non-genetic environmental effects. We further used genome‐wide association analysis to identify genomic regions associated with TL variation. We identified several putative genes underlying TL variation; these have been inferred to be involved in oxidative stress, cellular growth, skeletal development, cell differentiation and tumorigenesis in other species. Together, our results show that TL is a lowly heritable, polygenic trait which is strongly affected by environmental conditions in a free-living bird.

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Common Susceptibility Loci for Male Breast Cancer

JNCI Journal of the National Cancer Institute ◽

10.1093/jnci/djaa101 ◽

2020 ◽

Author(s):

Sarah Maguire ◽

Eleni Perraki ◽

Katarzyna Tomczyk ◽

Michael E Jones ◽

Olivia Fletcher ◽

...

Keyword(s):

Breast Cancer ◽

Association Study ◽

Genetic Correlation ◽

Male Breast Cancer ◽

Genetic Basis ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Susceptibility Loci ◽

Single Nucleotide ◽

Genome Wide

Abstract Background The etiology of male breast cancer (MBC) is poorly understood. In particular, the extent to which the genetic basis of MBC differs from female breast cancer (FBC) is unknown. A previous genome-wide association study of MBC identified 2 predisposition loci for the disease, both of which were also associated with risk of FBC. Methods We performed genome-wide single nucleotide polymorphism genotyping of European ancestry MBC case subjects and controls in 3 stages. Associations between directly genotyped and imputed single nucleotide polymorphisms with MBC were assessed using fixed-effects meta-analysis of 1380 cases and 3620 controls. Replication genotyping of 810 cases and 1026 controls was used to validate variants with P values less than 1 × 10–06. Genetic correlation with FBC was evaluated using linkage disequilibrium score regression, by comprehensively examining the associations of published FBC risk loci with risk of MBC and by assessing associations between a FBC polygenic risk score and MBC. All statistical tests were 2-sided. Results The genome-wide association study identified 3 novel MBC susceptibility loci that attained genome-wide statistical significance (P < 5 × 10–08). Genetic correlation analysis revealed a strong shared genetic basis with estrogen receptor–positive FBC. Men in the top quintile of genetic risk had a fourfold increased risk of breast cancer relative to those in the bottom quintile (odds ratio = 3.86, 95% confidence interval = 3.07 to 4.87, P = 2.08 × 10–30). Conclusions These findings advance our understanding of the genetic basis of MBC, providing support for an overlapping genetic etiology with FBC and identifying a fourfold high-risk group of susceptible men.

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Swedish Population Substructure Revealed by Genome-Wide Single Nucleotide Polymorphism Data

PLoS ONE ◽

10.1371/journal.pone.0016747 ◽

2011 ◽

Vol 6 (2) ◽

pp. e16747 ◽

Cited By ~ 24

Author(s):

Elina Salmela ◽

Tuuli Lappalainen ◽

Jianjun Liu ◽

Pertti Sistonen ◽

Peter M. Andersen ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Population Substructure ◽

Single Nucleotide Polymorphism Data ◽

Nucleotide Polymorphism ◽

Swedish Population ◽

Single Nucleotide ◽

Genome Wide ◽

Polymorphism Data

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Genome-Wide Association Study of Body Weight Traits in Chinese Fine-Wool Sheep

Animals ◽

10.3390/ani10010170 ◽

2020 ◽

Vol 10 (1) ◽

pp. 170 ◽

Cited By ~ 2

Author(s):

Zengkui Lu ◽

Yaojing Yue ◽

Chao Yuan ◽

Jianbin Liu ◽

Zhiqiang Chen ◽

...

Keyword(s):

Body Weight ◽

Muscle Development ◽

Genome Wide Association Study ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genome Wide ◽

Economic Trait ◽

Significance Levels ◽

Genomic Regions ◽

Selection Of

Body weight is an important economic trait for sheep and it is vital for their successful production and breeding. Therefore, identifying the genomic regions and biological pathways that contribute to understanding variability in body weight traits is significant for selection purposes. In this study, the genome-wide associations of birth, weaning, yearling, and adult weights of 460 fine-wool sheep were determined using resequencing technology. The results showed that 113 single nucleotide polymorphisms (SNPs) reached the genome-wide significance levels for the four body weight traits and 30 genes were annotated effectively, including AADACL3, VGF, NPC1, and SERPINA12. The genes annotated by these SNPs significantly enriched 78 gene ontology terms and 25 signaling pathways, and were found to mainly participate in skeletal muscle development and lipid metabolism. These genes can be used as candidate genes for body weight in sheep, and provide useful information for the production and genomic selection of Chinese fine-wool sheep.

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Population Differentiation at the HLA Genes

10.1101/214668 ◽

2017 ◽

Author(s):

Débora Y. C. Brandt ◽

Jônatas César ◽

Jérôme Goudet ◽

Diogo Meyer

Keyword(s):

Population Differentiation ◽

Balancing Selection ◽

Global Scale ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Hla Genes ◽

Genome Wide ◽

Different Populations ◽

Genomic Regions

ABSTRACTBalancing selection is defined as a class of selective regimes that maintain polymorphism above what is expected under neutrality. Theory predicts that balancing selection reduces population differentiation, as measured by FST. However, balancing selection regimes in which different sets of alleles are maintained in different populations could increase population differentiation. To tackle this issue, we investigated population differentiation at the HLA genes, which constitute the most striking example of balancing selection in humans. We found that population differentiation of single nucleotide polymorphisms (SNPs) at the HLA genes is on average lower than that of SNPs in other genomic regions. However, this result depends on accounting for the differences in allele frequency between selected and putatively neutral sites. Our finding of reduced differentiation at SNPs within HLA genes suggests a predominant role of shared selective pressures among populations at a global scale. However, in pairs of closely related populations, where genome-wide differentiation is low, differentiation at HLA is higher than in other genomic regions. This pattern was reproduced in simulations of overdominant selection. We conclude that population differentiation at the HLA genes is generally lower than genome-wide, but it may be higher for recently diverged population pairs, and that this pattern can be explained by a simple overdominance regime.

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Increased individual homozygosity is correlated with low fitness in a fragmented lizard population

Biological Journal of the Linnean Society ◽

10.1093/biolinnean/blz144 ◽

2019 ◽

Vol 128 (4) ◽

pp. 952-962 ◽

Cited By ~ 1

Author(s):

Javier Pérez-Tris ◽

Alejandro Llanos-Garrido ◽

Paul Bloor ◽

Roberto Carbonell ◽

José Luis Tellería ◽

...

Keyword(s):

Gene Flow ◽

Restricted Gene Flow ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genome Wide ◽

Anthropogenic Habitat ◽

Geographical Scale ◽

Psammodromus Algirus ◽

Fragmented Population ◽

The Impact

Abstract Isolation owing to anthropogenic habitat fragmentation is expected to increase the homozygosity of individuals, which might reduce their fitness as a result of inbreeding depression. Using samples from a fragmented population of the lizard Psammodromus algirus, for which we had data about two correlates of fitness, we genotyped individuals for six microsatellite loci that correctly capture genome-wide individual homozygosity of these lizards (as validated with an independent sample of lizards genotyped for both these microsatellites and > 70 000 single nucleotide polymorphisms). Our data revealed genetic structure at a very small geographical scale, which was compatible with restricted gene flow among populations disconnected in a matrix of inhospitable habitat. Lizards from the same fragment were genetically more related to one another than expected by chance, and individual homozygosity was greater in small than in large fragments. Within fragments, individual homozygosity was negatively associated with adult body size and clutch mass, revealing a link among reduced gene flow, increased homozygosity and lowered fitness that might reduce population viability deterministically. Our results contribute to mounting evidence of the impact of the loss of genetic diversity on fragmented wild populations.

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