scholarly journals Genomic analysis reveals a polygenic architecture of antler morphology in wild red deer (Cervus elaphus)

2021 ◽  
Author(s):  
Lucy Peters ◽  
Jisca Huisman ◽  
Loeske E.B. Kruuk ◽  
Josephine M. Pemberton ◽  
Susan E. Johnston
Keyword(s):  
Genetic Variation ◽  
Cervus Elaphus ◽  
Genetic Architecture ◽  
Empirical Bayes ◽  
Red Deer ◽  
Genetic Correlations ◽  
Rapid Evolution ◽  
Genomic Analysis ◽  
Sexually Selected Traits ◽  
Selected Traits

AbstractSexually-selected traits show large variation and rapid evolution across the animal kingdom, yet genetic variation often persists within populations despite apparent directional selection. A key step in solving this long-standing paradox is to determine the genetic architecture of sexually-selected traits to understand evolutionary drivers and constraints at the genomic level. Antlers are a form of sexual weaponry in male red deer. On the island of Rum, Scotland, males with larger antlers have increased breeding success, yet there has been no response to selection observed at the genetic level. To better understand the underlying mechanisms of this observation, we investigate the genetic architecture of ten antler traits and their principle components using genomic data from >38,000 SNPs. We estimate the heritabilities and genetic correlations of the antler traits using a genomic relatedness approach. We then use genome-wide association and haplotype-based regional heritability to identify regions of the genome underlying antler morphology, and an Empirical Bayes approach to estimate the underlying distributions of allele effect sizes. We show that antler morphology is heritable with a polygenic architecture, highly repeatable over an individual’s lifetime, and that almost all aspects are positively genetically correlated with some loci identified as having pleiotropic effects. Our findings suggest that a large mutational target and pleiotropy with traits sharing similar complex polygenic architectures are likely to contribute to the maintenance of genetic variation in antler morphology in this population.

scholarly journals Genetic variation and structure in Scandinavian red deer (Cervus elaphus): influence of ancestry, past hunting, and restoration management

2013 ◽  
Vol 109 (1) ◽  
pp. 43-53 ◽  
Author(s):  
Jacob Höglund ◽  
Maria Cortazar-Chinarro ◽  
Anders Jarnemo ◽  
Carl-Gustaf Thulin
Keyword(s):  
Genetic Variation ◽  
Cervus Elaphus ◽  
Red Deer ◽  
Restoration Management

scholarly journals Localizing components of shared transethnic genetic architecture of complex traits from GWAS summary data

2019 ◽  
Author(s):  
Huwenbo Shi ◽  
Kathryn S. Burch ◽  
Ruth Johnson ◽  
Malika K. Freund ◽  
Gleb Kichaev ◽  
...  
Keyword(s):  
Complex Traits ◽  
Genetic Architecture ◽  
Empirical Bayes ◽  
Genetic Correlations ◽  
Causal Snps ◽  
European Ancestry ◽  
Risk Scores ◽  
Common Snps ◽  
Genome Wide ◽  
Summary Data

AbstractDespite strong transethnic genetic correlations reported in the literature for many complex traits, the non-transferability of polygenic risk scores across populations suggests the presence of population-specific components of genetic architecture. We propose an approach that models GWAS summary data for one trait in two populations to estimate genome-wide proportions of population-specific/shared causal SNPs. In simulations across various genetic architectures, we show that our approach yields approximately unbiased estimates with in-sample LD and slight upward-bias with out-of-sample LD. We analyze 9 complex traits in individuals of East Asian and European ancestry, restricting to common SNPs (MAF > 5%), and find that most common causal SNPs are shared by both populations. Using the genome-wide estimates as priors in an empirical Bayes framework, we perform fine-mapping and observe that high-posterior SNPs (for both the population-specific and shared causal configurations) have highly correlated effects in East Asians and Europeans. In population-specific GWAS risk regions, we observe a 2.8x enrichment of shared high-posterior SNPs, suggesting that population-specific GWAS risk regions harbor shared causal SNPs that are undetected in the other GWAS due to differences in LD, allele frequencies, and/or sample size. Finally, we report enrichments of shared high-posterior SNPs in 53 tissue-specific functional categories and find evidence that SNP-heritability enrichments are driven largely by many low-effect common SNPs.

scholarly journals Genomic analysis reveals a polygenic architecture of antler morphology in wild red deer (Cervus elaphus)

2021 ◽  
Author(s):  
Lucy Peters ◽  
Jisca Huisman ◽  
Loeske E.B. Kruuk ◽  
Josephine M. Pemberton ◽  
Susan E. Johnston
Keyword(s):  
Cervus Elaphus ◽  
Red Deer ◽  
Genomic Analysis

scholarly journals Evolutionary rates for multivariate traits: the role of selection and genetic variation

2014 ◽  
Vol 369 (1649) ◽  
pp. 20130252 ◽  
Author(s):  
William Pitchers ◽  
Jason B. Wolf ◽  
Tom Tregenza ◽  
John Hunt ◽  
Ian Dworkin
Keyword(s):  
Evolutionary Biology ◽  
Genetic Architecture ◽  
Genetic Variance ◽  
Evolutionary Rates ◽  
Phenotypic Traits ◽  
Sexually Selected Traits ◽  
Rates Of Evolution ◽  
Selected Traits ◽  
Multivariate Traits

A fundamental question in evolutionary biology is the relative importance of selection and genetic architecture in determining evolutionary rates. Adaptive evolution can be described by the multivariate breeders' equation ( ), which predicts evolutionary change for a suite of phenotypic traits ( ) as a product of directional selection acting on them ( β ) and the genetic variance–covariance matrix for those traits ( G ). Despite being empirically challenging to estimate, there are enough published estimates of G and β to allow for synthesis of general patterns across species. We use published estimates to test the hypotheses that there are systematic differences in the rate of evolution among trait types, and that these differences are, in part, due to genetic architecture. We find some evidence that sexually selected traits exhibit faster rates of evolution compared with life-history or morphological traits. This difference does not appear to be related to stronger selection on sexually selected traits. Using numerous proposed approaches to quantifying the shape, size and structure of G , we examine how these parameters relate to one another, and how they vary among taxonomic and trait groupings. Despite considerable variation, they do not explain the observed differences in evolutionary rates.

Cloning and characterisation of the gene encoding red deer (Cervus elaphus) growth hormone: implications for the molecular evolution of growth hormone in artiodactyls

1997 ◽  
Vol 19 (3) ◽  
pp. 259-266 ◽  
Author(s):  
A Lioupis ◽  
OC Wallis ◽  
M Wallis
Keyword(s):  
Growth Hormone ◽  
Molecular Evolution ◽  
Cervus Elaphus ◽  
Red Deer ◽  
Signal Sequence ◽  
Rapid Evolution ◽  
Gene Encoding ◽  
Rate Of Evolution ◽  
Gh Gene ◽  
Polymerase Chain

In mammals the structure of pituitary GH is generally strongly conserved, indicating a slow basal rate of molecular evolution. However, on two occasions, during the evolution of primates and of artiodactyls, the rate of evolution has increased dramatically (25- to 50-fold) so that the sequences of human and ruminant GHs differ markedly from those of other mammalian GHs. In order to define further the burst of GH evolution that occurred in artiodactyls we have cloned and characterised the GH gene of red deer (Cervus elaphus) using genomic DNA and a polymerase chain reaction technique. The deduced sequence for the mature GH from red deer is identical to that of bovine GH, indicating that the burst of rapid evolution of GH that occurred in Artiodactyla must have been completed before the divergence of Cervidae and Bovidae and suggesting that the rate of evolution during this burst must have been greater than previously estimated. In other aspects (signal sequence, 5' and 3' sequences, introns and synonymous substitutions in the coding sequence) the red deer GH gene differs considerably from the GH genes of other ruminants. Differences between the signal peptide sequences of red deer and bovid GHs probably explain why N-terminal heterogeneity is seen in bovine, ovine and caprine GHs but not GH from red deer, pig or most other mammals.

scholarly journals A genomic region containing REC8 and RNF212B is associated with individual recombination rate variation in a wild population of red deer (Cervus elaphus)

2018 ◽  
Author(s):  
Susan E. Johnston ◽  
Jisca Huisman ◽  
Josephine M. Pemberton
Keyword(s):  
Linkage Group ◽  
Cervus Elaphus ◽  
Recombination Rate ◽  
Genetic Architecture ◽  
Red Deer ◽  
Wild Population ◽  
Genomic Region ◽  
Rate Variation ◽  
Phenotypic Variance ◽  
Recombination Rate Variation

AbstractRecombination is a fundamental feature of sexual reproduction, ensuring proper disjunction, preventing mutation accumulation and generating new allelic combinations upon which selection can act. However it is also mutagenic, and breaks up favourable allelic combinations previously built up by selection. Identifying the genetic drivers of recombination rate variation is a key step in understanding the causes and consequences of this variation, how lociassociated with recombination are evolving and how they affect the potential of a population to respond to selection. However, to date, few studies have examined the genetic architecture of recombination rate variation in natural populations. Here, we use pedigree data from ‐2,600 individuals genotyped at ‐38,000 SNPs to investigate the genetic architecture of individual autosomal recombination rate in a wild population of red deer (Cervus elaphus). Female red deer exhibited a higher mean and phenotypic variance in autosomal crossover counts (ACC). Animal models fitting genomic relatedness matrices showed that ACC was heritable in females (h2 = 0.12) but not in males. A regional heritability mapping approach showed that almost all heritable variation in female ACC was explained by a genomic region on deer linkage group 12 containing the candidate loci REC8 and RNF212B, with an additional region on linkage group 32 containing TOP2B approaching genome-wide significance. The REC8/RNF212B region and its paralogue RNF212 have been associated with recombination in cattle, mice, humans and sheep. Our findings suggest that mammalian recombination rates have a relatively conserved genetic architecture in both domesticated and wild systems, and provide a foundation for understanding the association between recombination lociand individual fitness within this population.

scholarly journals A conserved trans regulatory loop involving an odorant binding protein controls male mating behavior in flies

2021 ◽  
Author(s):  
Pablo J Delclos ◽  
Kiran Adhikari ◽  
Oluwatomi Hassan ◽  
Alexander A Oderhowho ◽  
Vyshnika Sriskantharajah ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Mating Behavior ◽  
House Fly ◽  
Male Mating ◽  
Sexually Selected Traits ◽  
Y Chromosomes ◽  
Male Mating Behavior ◽  
Selected Traits ◽  
Regulatory Loop ◽  
Odorant Binding

A major goal in evolutionary biology is to understand how natural variation is maintained in sexually selected and sexually dimorphic traits. Hypotheses to explain genetic variation in sexually selected traits include context-dependent fitness effects, epistatic interactions, and pleiotropic constraints. The house fly, Musca domestica, is a promising system to investigate how these factors affect polymorphism in sexually selected traits. Two common Y chromosomes (YM and IIIM) segregate as stable polymorphisms in natural house fly populations, appear to be locally adapted to different thermal habitats, and differentially affect male mating success. Here, we perform a meta-analysis of RNA-seq data which identifies genes encoding odorant binding proteins (in the Obp56h family) as differentially expressed between the heads of males carrying YM and IIIM. Differential expression of Obp56h has been associated with variation in male mating behavior in Drosophila melanogaster. We find differences in male mating behavior between house flies carrying the Y chromosomes that are consistent with the relationship between male mating behavior and expression of Obp56h in D. melanogaster. We also find that male mating behaviors in house fly are affected by temperature, and the same temperature differentials further affect the expression of Obp56h genes. However, we show that temperature-dependent effects cannot explain the maintenance of genetic variation for male mating behavior in house fly. Using a network analysis and allele-specific expression measurements, we find evidence that the house fly IIIM chromosome is a trans regulator of Obp56h gene expression. Moreover, we find that Obp56h disproportionately affects the expression of genes on the D. melanogaster chromosome that is homologous to the house fly IIIM chromosome. This provides evidence for a conserved trans regulatory loop involving Obp56h expression that affects male mating behavior in flies. The complex regulatory architecture controlling Obp56h expression suggests that variation in male mating behavior could be maintained by epistasis or pleiotropic constraints.

scholarly journals Intensive Management and Natural Genetic Variation in Red Deer (Cervus elaphus)

2017 ◽  
Vol 108 (5) ◽  
pp. 496-504 ◽  
Author(s):  
Juan A. Galarza ◽  
Beatriz Sánchez-Fernández ◽  
Paulino Fandos ◽  
Ramón Soriguer
Keyword(s):  
Genetic Variation ◽  
Cervus Elaphus ◽  
Red Deer ◽  
Intensive Management ◽  
Natural Genetic Variation

scholarly journals Evolutionary rates for multivariate traits: the role of selection and genetic variation

2014 ◽  
Author(s):  
William Pitchers ◽  
Jason B. Wolf ◽  
Tom Tregenza ◽  
John Hunt ◽  
Ian Dworkin
Keyword(s):  
Evolutionary Biology ◽  
Genetic Architecture ◽  
Genetic Variance ◽  
Evolutionary Rates ◽  
Phenotypic Traits ◽  
Sexually Selected Traits ◽  
Rates Of Evolution ◽  
Selected Traits ◽  
Multivariate Traits

A fundamental question in evolutionary biology is the relative importance of selection and genetic architecture in determining evolutionary rates. Adaptive evolution can be described by the multivariate breeders' equation (Δz = Gβ), which predicts evolutionary change for a suite of phenotypic traits (Δz) as a product of directional selection acting on them (β) and the genetic variance-covariance matrix for those traits (G). Despite being empirically challenging to estimate, there are enough published estimates ofGandβto allow for synthesis of general patterns across species. We use published estimates to test the hypotheses that there are systematic differences in the rate of evolution among trait types, and that these differences are in part due to genetic architecture. We find evidence that sexually selected traits exhibit faster rates of evolution compared to life-history or morphological traits. This difference does not appear to be related to stronger selection on sexually selected traits. Using numerous proposed approaches to quantifying the shape, size and structure ofGwe examine how these parameters relate to one another, and how they vary among taxonomic and trait groupings. Despite considerable variation, they do not explain the observed differences in evolutionary rates.

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