Taking quantitative genomics into the wild

Johnston, Susan E.; Chen, Nancy; Josephs, Emily B.

doi:10.1098/rspb.2022.1930

Cited by 10 publications

(16 citation statements)

References 138 publications

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“…Investigating this contribution will be highly challenging, but future research in this area may provide the power and possibility to test this hypothesis. Finally, whilst the marker density we used here is high relative to the observed decay in linkage disequilibrium, we acknowledge that a lack of association with GWAS can also arise due to reduced power to detect trait loci, due to relatively small sample sizes compared to human and livestock studies (Santure and Garant 2018; Johnston et al . 2022).…”

Section: Discussionmentioning

confidence: 99%

The genetic architecture of recombination rates is polygenic and differs between the sexes in wild house sparrows (Passer domesticus)

McAuley

Servin

Peters

et al. 2023

Preprint

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Meiotic recombination is a fundamental feature of sex and an important driver of diversity in eukaryotic genomes. It ensures proper chromosome disjunction, increases responses to selection, and prevents mutation accumulation; however, it is also mutagenic and can break up favourable haplotypes built up by selection. This cost/benefit dynamic is likely to vary depending on mechanistic and evolutionary contexts, and indeed, recombination rates show huge variation within and between chromosomes, individuals, sexes, populations and species. Identifying the genetic architecture of recombination rates is a key step in understanding the causes and consequences of this variation. Here, we investigate broad-scale recombination landscapes and individual crossover (CO) rates in a wild population of house sparrows (Passer domesticus). We integrated pedigree data with ~61K SNPs to identify autosomal crossover counts (ACC) and intra-chromosomal allelic shuffling (r¯intra) in 2,802 gametes. Females had longer autosomal genetic maps (2,558.1cM vs 2,069.6cM), 1.37 times higher ACC, and 1.46 times higherr¯intrathan males. ACC was heritable in females (h2= 0.23) but not in males, indicating genetic independence of male and female crossover rates. Conversely,r¯intrawas heritable in males (h2= 0.07), but not in females. Neither measure was associated with age or common environment effects. Genome-wide association studies of female ACC and maler¯intrafound no loci explaining more than XX% of additive genetic variation, but ~2% of SNPs had non-zero effects on female ACC. Our results suggest that recombination rates in house sparrows are polygenic and driven by many small-effect loci that may act in cis (e.g. local recombination hotspots) or trans (global recombination modifiers). This work shows that recombination rates have evolutionary potential in wild birds, and provides a foundation for understanding associations between recombination rates, genome architecture, and individual fitness.

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Section: Discussionmentioning

confidence: 99%

The genetic architecture of recombination rates is polygenic and differs between the sexes in wild house sparrows (Passer domesticus)

McAuley

Servin

Peters

et al. 2023

Preprint

Self Cite

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“…This study adds to a series of recent work using large sets of molecular markers to study quantitative genetics in wild populations, mostly focused on animals [ 69 ], but also on plants [ 47 , 70 ]. Studies comparing the accuracy of SNP-based relatedness matrices compared to pedigrees are consistently showing that they can be very good approximations of continuous genetic relatedness, depending on the specie's life history, and that they can provide higher analytical flexibility [ 69 , 71 , 72 ].…”

Section: Discussionmentioning

confidence: 99%

Quantitative genetic analysis of floral traits shows current limits but potential evolution in the wild

et al. 2023

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The vast variation in floral traits across angiosperms is often interpreted as the result of adaptation to pollinators. However, studies in wild populations often find no evidence of pollinator-mediated selection on flowers. Evolutionary theory predicts this could be the outcome of periods of stasis under stable conditions, followed by shorter periods of pollinator change that provide selection for innovative phenotypes. We asked if periods of stasis are caused by stabilizing selection, absence of other forms of selection or by low trait ability to respond even if selection is present. We studied a plant predominantly pollinated by one bee species across its range. We measured heritability and evolvability of traits, using genome-wide relatedness in a large wild population, and combined this with estimates of selection on the same individuals. We found evidence for both stabilizing selection and low trait heritability as potential explanations for stasis in flowers. The area of the standard petal is under stabilizing selection, but the variability is not heritable. A separate trait, floral weight, presents high heritability, but is not currently under selection. We show how a simple pollination environment coincides with the absence of current prerequisites for adaptive evolutionary change, while heritable variation remains to respond to future selection pressures.

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“…The requirement of pedigree information for quantitative trait loci (QTL) and genome wide association studies (GWAS) also provides a limitation to their usage in wild populations (Day-Williams et al, 2011). Recent advances have softened this requirement, with several routes available for quantitative genetic analyses in wild populations where pedigree information is absent (Johnston et al, 2022). Finally, where the genetic basis of morphological traits is known, signatures of past selection can be detected through phylogenetic analysis (Vitti et al, 2013).…”

Section: Linking Morphology To Geneticsmentioning

confidence: 99%

The genetics-morphology-behaviour trifecta: unravelling the single greatest limitation affecting our understanding of chondrichthyan evolution

Gayford

2023

Preprint

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Sharks, rays and chimaera form the clade Chondrichthyes, an ancient group of morphologically and ecologically diverse vertebrates that has played an important role in our understanding of gnathostome evolution. Increasingly studies have are seeking to investigate evolutionary processes operating within the chondrichthyan crown group, with the broad aim of understanding the driving forces behind the vast phenotypic diversity observed amongst its constituent taxa. Genetic, morphological and behavioural studies have all contributed to our understanding of phenotypic evolution yet are typically considered in isolation in the context of Chondrichthyes. I argue that integrating these core fields of organismal biology is vital if we are to understand the evolutionary processes operating in contemporary chondrichthyan taxa, and how such processes have contributed to past phenotypic evolution. In light of the global extinction crisis facing this clade, this understanding is crucial if we are to successfully conserve rapidly declining chondrichthyan populations.

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Taking quantitative genomics into the wild

Cited by 10 publications

References 138 publications

The genetic architecture of recombination rates is polygenic and differs between the sexes in wild house sparrows (Passer domesticus)

The genetic architecture of recombination rates is polygenic and differs between the sexes in wild house sparrows (Passer domesticus)

Quantitative genetic analysis of floral traits shows current limits but potential evolution in the wild

The genetics-morphology-behaviour trifecta: unravelling the single greatest limitation affecting our understanding of chondrichthyan evolution

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