Detection of sexually antagonistic transmission distortions in trio datasets

ABSTRACTSex dimorphisms are widespread in animals and plants, for morphological as well as physiological traits. Understanding the genetic basis of sex dimorphism and its evolution is crucial for understanding biological differences between the sexes. Genetic variants with sex-antagonistic effects on fitness are expected to segregate in populations at the early phases of sexual dimorphism emergence. Detecting such variants is notoriously difficult, and the few genome-scan methods employed so far have limited power and little specificity. Here, we propose a new framework to detect a signature of sexually antagonistic selection. We rely on trio datasets where sex-biased transmission distortions can be directly tracked from parents to offspring, and allows identifying signal of sexually antagonistic transmission distortions in genomic regions. We report the genomic location and recombination pattern surrounding 66 regions detected as potentially under sexually antagonist selection. We find an enrichment of genes associated with embryonic development within these regions. Last, we highlight two candidates regions for sexually antagonistic selection in humans.

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Development of a Set of Microsatellite Markers to Investigate Sexually Antagonistic Selection in the Invasive Ant Nylanderia fulva

Insects ◽

10.3390/insects12070643 ◽

2021 ◽

Vol 12 (7) ◽

pp. 643

Author(s):

Pierre-Andre Eyer ◽

Megan N. Moran ◽

Alexander J. Blumenfeld ◽

Edward L. Vargo

Keyword(s):

Microsatellite Markers ◽

Genomic Region ◽

Antagonistic Selection ◽

Origin And Evolution ◽

Introduced Range ◽

Nylanderia Fulva ◽

Sexually Antagonistic Selection ◽

Males And Females ◽

Native And Introduced Ranges ◽

Genomic Regions

Sexually antagonistic selection (SAS) occurs when distinct alleles are differentially selected in each sex. In the invasive tawny crazy ant, Nylanderia fulva, a genomic region is under SAS, while the rest of the genome is randomly selected in males and females. In this study, we designed a suite of 15 microsatellite markers to study the origin and evolution of SAS in N. fulva. These SAS markers were polymorphic, with allelic frequencies that are highly different between males and females. All haploid males carry only a subset of the alleles present in the population, while females are reliably heterozygous, with one allele from the male gene pool and a different allele inherited from their mother. In addition, we identified six polymorphic markers not associated with SAS and six markers yielding consistent, yet monomorphic, amplification in the introduced range of this species. Reaction condition optimizations allowed all retained markers to be co-amplified in four PCR mixes. The SAS markers may be used to test for the strength and the extent of the genomic regions under SAS in both the native and introduced ranges of N. fulva, while the set of non-SAS loci may be used to assess the invasion route of this species. Overall, the application of these microsatellite markers will yield insights into the origin and evolution of SAS within and among species of the genus Nylanderia.

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Race on Both Sides of the Razor

Kalfou A Journal of Comparative and Relational Ethnic Studies ◽

10.15367/kf.v5i1.194 ◽

2018 ◽

Vol 5 (1) ◽

Cited By ~ 1

Author(s):

Terence D. Keel

Keyword(s):

Social Constructionism ◽

Political Correctness ◽

Genetic Basis ◽

Genetic Research ◽

Scientific Progress ◽

Social Constructionist ◽

Behavioral Differences ◽

Social Activists ◽

Continued Use ◽

Biological Differences

The proliferation of studies declaring that there is a genetic basis to health disparities and behavioral differences across the so-called races has encouraged the opponents of social constructionism to assert a victory for scientific progress over political correctness. I am not concerned in this essay with providing a response to critics who believe races are expressions of innate genetic or biological differences. Instead, I am interested in how genetic research on human differences has divided social constructionists over whether the race concept in science can be used for social justice and redressing embodied forms of discrimination. On one side, there is the position that race is an inherently flawed concept and that its continued use by scientists, medical professionals, and even social activists keeps alive the notion that it has a biological basis. On the other side of this debate are those who maintain a social constructionist position yet argue that not all instances of race in science stem from discriminatory politics or the desire to prove that humans belong to discrete biological units that can then be classified as superior or inferior. I would like to shift this debate away from the question of whether race is real and move instead toward thinking about the intellectual commitments necessary for science to expose past legacies of discrimination.

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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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The X chromosome favors males under sexually antagonistic selection

Evolution ◽

10.1111/evo.13646 ◽

2018 ◽

Vol 73 (1) ◽

pp. 84-91 ◽

Cited By ~ 10

Author(s):

Manus M. Patten

Keyword(s):

X Chromosome ◽

Antagonistic Selection ◽

Sexually Antagonistic Selection

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LIVE FAST, DIE YOUNG: TRADE-OFFS BETWEEN FITNESS COMPONENTS AND SEXUALLY ANTAGONISTIC SELECTION ON WEAPONRY IN SOAY SHEEP

Evolution ◽

10.1111/j.0014-3820.2006.tb01854.x ◽

2006 ◽

Vol 60 (10) ◽

pp. 2168-2181 ◽

Cited By ~ 96

Author(s):

Matthew R. Robinson ◽

Jill G. Pilkington ◽

Tim H. Clutton-Brock ◽

Josephine M. Pemberton ◽

Loeske E.B. Kruuk

Keyword(s):

Fitness Components ◽

Antagonistic Selection ◽

Soay Sheep ◽

Trade Offs ◽

Sexually Antagonistic Selection

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dbVar structural variant cluster set for data analysis and variant comparison

F1000Research ◽

10.12688/f1000research.8290.1 ◽

2016 ◽

Vol 5 ◽

pp. 673 ◽

Cited By ~ 10

Author(s):

Lon Phan ◽

Jeffrey Hsu ◽

Le Quang Minh Tri ◽

Michaela Willi ◽

Tamer Mansour ◽

...

Keyword(s):

Genomic Sequence ◽

Chromosomal Rearrangements ◽

Copy Number Variations ◽

Structural Variant ◽

Variant Type ◽

External Data ◽

Cluster Set ◽

Genomic Location ◽

Complex Chromosomal Rearrangements ◽

Genomic Regions

dbVar houses over 3 million submitted structural variants (SSV) from 120 human studies including copy number variations (CNV), insertions, deletions, inversions, translocations, and complex chromosomal rearrangements. Users can submit multiple SSVs to dbVAR that are presumably identical, but were ascertained by different platforms and samples, to calculate whether the variant is rare or common in the population and allow for cross validation. However, because SSV genomic location reporting can vary – including fuzzy locations where the start and/or end points are not precisely known – analysis, comparison, annotation, and reporting of SSVs across studies can be difficult. This project was initiated by the Structural Variant Comparison Group for the purpose of generating a non-redundant set of genomic regions defined by counts of concordance for all human SSVs placed on RefSeq assembly GRCh38 (RefSeq accession GCF_000001405.26). We intend that the availability of these regions, called structural variant clusters (SVCs), will facilitate the analysis, annotation, and exchange of SV data and allow for simplified display in genomic sequence viewers for improved variant interpretation. Sets of SVCs were generated by variant type for each of the 120 studies as well as for a combined set across all studies. Starting from 3.64 million SSVs, 2.5 million and 3.4 million non-redundant SVCs with count >=1 were generated by variant type for each study and across all studies, respectively. In addition, we have developed utilities for annotating, searching, and filtering SVC data in GVF format for computing summary statistics, exporting data for genomic viewers, and annotating the SVC using external data sources.

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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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