Demographic History, Not Mating System, Explains Signatures of Inbreeding and Inbreeding Depression in a Large Outbred Population

Sin, Simon Yung Wa; Hoover, Brian A.; Nevitt, Gabrielle A.; Edwards, Scott V.

doi:10.1086/714079

Cited by 13 publications

(18 citation statements)

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“…Admixture between populations with different allele frequencies causes gametic associations (i.e., LD) between loci as a function of the difference between the parental populations and the admixture rate (Chakraborty & Weiss, 1988) and the effects of admixture can be variable and can either increase or decrease GWH depending on the magnitude of admixture and the genetic background of the population (Vendrami et al, 2020). Importantly, in both red deer and storm petrel where variance in inbreeding was less than seen recently in Rio Grande silvery minnow, general effects HFC were observed implying inbreeding depression in both a small (Huisman et al, 2016) and a large population (Sin et al, 2021). Hence, inclusion of inbreeding metrics in genetic monitoring of both wild and captive populations of Rio Grande silvery minnow can provide valuable information for adaptive management of the species (e.g., altered augmentation strategies).…”

Section: Discussionmentioning

confidence: 86%

“…Like Rio Grande silvery minnow, the population of deer has experienced bottlenecks and admixture between different populations (Huisman et al, 2016). Sin et al (2021) noted that in storm petrel, mating system and inbreeding between close relatives could not account for variance in inbreeding, and hence, suggested that observed variance in inbreeding was explained by past population bottlenecks along with more recent declines in N e and low levels of admixture between Atlantic and Pacific populations of petrels. Footprints of bottlenecks persist even after the population has recovered (Bierne et al, 2000) and can still cause inbreeding depression (Sin et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

“…Importantly, in both red deer and storm petrel where variance in inbreeding was less than seen recently in Rio Grande silvery minnow, general effects HFC were observed implying inbreeding depression in both a small (Huisman et al, 2016) and a large population (Sin et al, 2021). Hence, inclusion of inbreeding metrics in genetic monitoring of both wild and captive populations of Rio Grande silvery minnow can provide valuable information for adaptive management of the species (e.g., altered augmentation strategies).…”

Section: Evaluation Of Inbreeding Metrics For Genetic Monitoringmentioning

confidence: 92%

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Transitioning from microsatellites to SNP‐based microhaplotypes in genetic monitoring programmes: Lessons from paired data spanning 20 years

2022

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Genetic monitoring quantifies trajectories of individual-and population-level metrics that include heterozygosity, gene diversity and genetic effective population size (N e ) over contemporary time series (Schwartz et al., 2007). Tracking these metrics facilitates adaptive and evolutionary-cognizant management. For the past three decades, microsatellites were the workhorse for genetic monitoring programmes (e.g., Beatty et al., 2014;Dowling et al., 2014;Koelewijn et al., 2010). Long-term monitoring programmes are now transitioning to next-generation high-throughput genomic approaches based on single-nucleotide polymorphisms (SNPs) and microhaplotypes (i.e., multiple SNPs haplotyped at the same locus); raising questions about continuity and consistency across the time series as well as

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Section: Discussionmentioning

confidence: 86%

Section: Discussionmentioning

confidence: 99%

Section: Evaluation Of Inbreeding Metrics For Genetic Monitoringmentioning

confidence: 92%

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Transitioning from microsatellites to SNP‐based microhaplotypes in genetic monitoring programmes: Lessons from paired data spanning 20 years

2022

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“…We also measured genome-wide heterozygosity at 2514 loci using restriction site-associated DNA sequencing for 312 adults [48]. We examined the relationship between MHC heterozygosity and genome-wide heterozygosity to determine whether genome-wide variation may explain the patterns between MHC and the chemical profiles.…”

Section: Methodsmentioning

confidence: 99%

Feather chemicals contain information about the major histocompatibility complex in a highly scented seabird

et al. 2022

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Mate choice informed by the immune genes of the major histocompatibility complex (MHC) may provide fitness benefits including offspring with increased immunocompetence. Olfactory cues are considered the primary mechanism organisms use to evaluate the MHC of potential mates, yet this idea has received limited attention in birds. Motivated by a finding of MHC-dependent mate choice in the Leach's storm-petrel ( Oceanodroma leucorhoa ), we examined whether the chemical profiles of this highly scented seabird contain information about MHC genes. Whereas previous studies in birds examined non-volatile compounds, we used gas chromatography–mass spectrometry to measure the volatile compounds emitted from feathers that potentially serve as olfactory infochemicals about MHC and coupled this with locus-specific genotyping of MHC IIB genes. We found that feather chemicals reflected individual MHC diversity through interactions with sex and breeding status. Furthermore, similarity in MHC genotype was correlated with similarity in chemical profiles within female–female and male–female dyads. We provide the first evidence that volatile chemicals from bird feathers can encode information about the MHC. Our findings suggest that olfaction likely aids MHC-based mate choice in this species and highlight a role for chemicals in mediating genetic mate choice in birds where this mode of communication has been largely overlooked.

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“…Variance in inbreeding is therefore essential for HFCs to be detected [6]. In addition, variance in inbreeding is interesting per se because it depends on both demographic history (e.g., [7]) and mating system (selfing, partial selfing or outcrossing) [8]. For mating system, selfers vs. outcrossers can show contrasting levels of inbreeding, with different consequences for genetic diversity, depending on population history.…”

Section: Introductionmentioning

confidence: 99%

Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus

et al. 2022

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Many studies have quantified the distribution of heterozygosity and relatedness in natural populations, but few have examined the demographic processes driving these patterns. In this study, we take a novel approach by studying how population structure affects both pairwise identity and the distribution of heterozygosity in a natural population of the self-incompatible plant Antirrhinum majus. Excess variance in heterozygosity between individuals is due to identity disequilibrium (ID), which reflects the variance in inbreeding between individuals; it is measured by the statistic g2. We calculated g2 together with FST and pairwise relatedness (Fij) using 91 SNPs in 22,353 individuals collected over 11 years. We find that pairwise Fij declines rapidly over short spatial scales, and the excess variance in heterozygosity between individuals reflects significant variation in inbreeding. Additionally, we detect an excess of individuals with around half the average heterozygosity, indicating either selfing or matings between close relatives. We use two types of simulation to ask whether variation in heterozygosity is consistent with fine-scale spatial population structure. First, by simulating offspring using parents drawn from a range of spatial scales, we show that the known pollen dispersal kernel explains g2. Second, we simulate a 1000-generation pedigree using the known dispersal and spatial distribution and find that the resulting g2 is consistent with that observed from the field data. In contrast, a simulated population with uniform density underestimates g2, indicating that heterogeneous density promotes identity disequilibrium. Our study shows that heterogeneous density and leptokurtic dispersal can together explain the distribution of heterozygosity.

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Demographic History, Not Mating System, Explains Signatures of Inbreeding and Inbreeding Depression in a Large Outbred Population

Cited by 13 publications

References 94 publications

Transitioning from microsatellites to SNP‐based microhaplotypes in genetic monitoring programmes: Lessons from paired data spanning 20 years

Transitioning from microsatellites to SNP‐based microhaplotypes in genetic monitoring programmes: Lessons from paired data spanning 20 years

Feather chemicals contain information about the major histocompatibility complex in a highly scented seabird

Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus

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