HIERARCHICAL ANALYSIS OF INBREEDING DEPRESSION IN PEROMYSCUS POLIONOTUS

The severity of inbreeding depression appears to vary among taxa, but few ecological or other patterns have been identified that predict accurately which taxa are most sensitive to inbreeding. To examine the causes of heterogeneity in inbreeding depression, the effects of inbreeding on reproduction, survival, and growth were measured in three replicate experimental stocks for each of three subspecies of Peromyscus polionotus mice. Inbreeding of the dam reduced the probability of breeding, the probability of producing a second litter, and litter size. Inbreeding of the litter caused depression of litter size, juvenile viability, and mass at weaning, and caused an increase in the within-litter variance in mass. In spite of differences between the subspecies in natural population sizes, genetic variation, and mean rates of reproduction and survival, all variation observed between experimental populations in their responses to inbreeding could be attributed to random founder effects. The genetic load of deleterious alleles in each replicate was unequally partitioned among its founder pairs, and different founders contributed to the load affecting different fitness components. Thus, inbreeding depression for any one fitness component, in our experimental environment, must be due to relatively few deleterious alleles with major effects. Genetic loads so comprised would be expected to diverge among natural populations due to both random drift and selective removal of recessive deleterious alleles during population bottlenecks. The near universality of inbreeding depression would be maintained, however, if different alleles contribute to inbreeding depression of different fitness components and in different environments.     

SEVERE INBREEDING DEPRESSION AND NO EVIDENCE OF PURGING IN AN EXTREMELY INBRED WILD SPECIES—THE CHATHAM ISLAND BLACK ROBIN

Although evidence of inbreeding depression in wild populations is well established, the impact of genetic purging in the wild remains controversial. The contrasting effects of inbreeding depression, fixation of deleterious alleles by genetic drift, and the purging of deleterious alleles via natural selection mean that predicting fitness outcomes in populations subjected to prolonged bottlenecks is not straightforward. We report results from a long‐term pedigree study of arguably the world's most inbred wild species of bird: the Chatham Island black robin Petroica traversi, in which conditions were ideal for purging to occur. Contrary to expectations, black robins showed a strong, negative relationship between inbreeding and juvenile survival, yielding lethal equivalents (2B) of 6.85. We also determined that the negative relationship between inbreeding and survival did not appear to be mediated by levels of ancestral inbreeding and may be attributed in part to unpurged lethal recessives. Although the black robin demographic history provided ideal conditions for genetic purging, our results show no clear evidence of purging in the major life‐history trait of juvenile survival. Our results also show no evidence of fixation of deleterious alleles in juvenile survival, but do confirm that continued high levels of contemporary inbreeding in a historically inbred population could lead to additional severe inbreeding depression.     

Inbreeding rate modifies the dynamics of genetic load in small populations

The negative fitness consequences of close inbreeding are widely recognized, but predicting the long-term effects of inbreeding and genetic drift due to limited population size is not straightforward. As the frequency and homozygosity of recessive deleterious alleles increase, selection can remove (purge) them from a population, reducing the genetic load. At the same time, small population size relaxes selection against mildly harmful mutations, which may lead to accumulation of genetic load. The efficiency of purging and the accumulation of mutations both depend on the rate of inbreeding (i.e., population size) and on the nature of mutations. We studied how increasing levels of inbreeding affect offspring production and extinction in experimental Drosophila littoralis populations replicated in two sizes, N = 10 and N = 40. Offspring production and extinction were measured over 25 generations concurrently with a large control population. In the N = 10 populations, offspring production decreased strongly at low levels of inbreeding, then recovered only to show a consistent subsequent decline, suggesting early expression and purging of recessive highly deleterious alleles and subsequent accumulation of mildly harmful mutations. In the N = 40 populations, offspring production declined only after inbreeding reached higher levels, suggesting that inbreeding and genetic drift pose a smaller threat to population fitness when inbreeding is slow. Our results suggest that highly deleterious alleles can be purged in small populations already at low levels of inbreeding, but that purging does not protect the small populations from eventual genetic deterioration and extinction.     

Analysis of founder representation in pedigrees: Founder equivalents and founder genome equivalents

The concepts of “founder equivalent” and “founder genome equivalent” are introduced to facilitate analysis of the founding stocks of captive or other populations for which pedigrees are available. The founder equivalents of a population are the number of equally contributing founders that would be expected to produce the same genetic diversity as in the population under study. Unequal genetic contributions by founders decrease the founder equivalents, portend greater inbreeding in future generations than would be necessary, and reflect a greater loss of the genetic diversity initially present in the founders. The number of founder genome equivalents of a population is that number of equally contributing founders with no random loss of founder alleles in descendants that would be expected to produce the same genetic diversity as in the population under study. The number of founder genome equivalents is approximately that number of wild-caught animals that would be needed to obtain the same amount of genetic diversity as is in the descendant captive population. Founder equivalents and founder genome equivalents allow comparison of the genetic merits of adding new wild-caught stock vs. further equalizing founder representations in a captive population.     

Temporal dynamics of genetic variability in a mountain goat (Oreamnos americanus) population

The association between population dynamics and genetic variability is of fundamental importance for both evolutionary and conservation biology. We combined long-term population monitoring and molecular genetic data from 123 offspring and their parents at 28 microsatellite loci to investigate changes in genetic diversity over 14 cohorts in a small and relatively isolated population of mountain goats (Oreamnos americanus) during a period of demographic increase. Offspring heterozygosity decreased while parental genetic similarity and inbreeding coefficients (F(IS) ) increased over the study period (1995-2008). Immigrants introduced three novel alleles into the population and matings between residents and immigrants produced more heterozygous offspring than local crosses, suggesting that immigration can increase population genetic variability. The population experienced genetic drift over the study period, reflected by a reduced allelic richness over time and an 'isolation-by-time' pattern of genetic structure. The temporal decline of individual genetic diversity despite increasing population size probably resulted from a combination of genetic drift due to small effective population size, inbreeding and insufficient counterbalancing by immigration. This study highlights the importance of long-term genetic monitoring to understand how demographic processes influence temporal changes of genetic diversity in long-lived organisms.     

Demographic and genetic effects on reproduction as related to population size in a rare, perennial herb, Senecio integrifolius (Asteraceae)

Seed-set of the rare and threatened plant Senecio integrifolius increased significantly with population size. Experimental studies as well as field observations showed this to be due to density-dependent seed-set (Allee effect). Hand-pollination revealed lower seed-set, and a lower germination rate of inbred progeny than of outbred progeny, with great differences among populations. Contrary to general predictions in models of minimum viable population sizes, the present study indicates little negative effects of inbreeding in small populations. A genetic load model was invoked to explain the results, hypothesizing that purging of deleterious alleles in small populations has reduced inbreeding depression. However, no clear correlation between population size and genetic load was found. The results in this paper suggest that demographic and environmental factors are of greater immediate importance than population genetics in determining extinction probabilities of small plant populations.     

Female mating preferences and offspring survival: testing hypotheses on the genetic basis of mate choice in a wild lekking bird

Indirect benefits of mate choice result from increased offspring genetic quality and may be important drivers of female behaviour. ‘Good‐genes‐for‐viability’ models predict that females prefer mates of high additive genetic value, such that offspring survival should correlate with male attractiveness. Mate choice may also vary with genetic diversity (e.g. heterozygosity) or compatibility (e.g. relatedness), where the female's genotype influences choice. The relative importance of these nonexclusive hypotheses remains unclear. Leks offer an excellent opportunity to test their predictions, because lekking males provide no material benefits and choice is relatively unconstrained by social limitations. Using 12 years of data on lekking lance‐tailed manakins, Chiroxiphia lanceolata, we tested whether offspring survival correlated with patterns of mate choice. Offspring recruitment weakly increased with father attractiveness (measured as reproductive success, RS), suggesting attractive males provide, if anything, only minor benefits via offspring viability. Both male RS and offspring survival until fledging increased with male heterozygosity. However, despite parent–offspring correlation in heterozygosity, offspring survival was unrelated to its own or maternal heterozygosity or to parental relatedness, suggesting survival was not enhanced by heterozygosity per se. Instead, offspring survival benefits may reflect inheritance of specific alleles or nongenetic effects. Although inbreeding depression in male RS should select for inbreeding avoidance, mates were not less related than expected under random mating. Although mate heterozygosity and relatedness were correlated, selection on mate choice for heterozygosity appeared stronger than that for relatedness and may be the primary mechanism maintaining genetic variation in this system despite directional sexual selection.     

When it comes to inbreeding: slower is better

The extent to which genetic diversity is lost from inbred populations is important for conservation biology, evolutionary ecology, and plant and animal breeding. This importance stems from the fact that the amount of genetic diversity a population has is expected to correlate with evolutionary potential. A population's ability to avert extinction during rapidly changing environmental conditions, or the magnitude of response to selection on a trait, depend on the ability of the genome to maintain potentially adaptive genetic variation in the face of random genetic drift. Although a few previous studies have demonstrated that the rate of inbreeding affects the amount of genetic diversity maintained, the elegant work of Demontis et al. , in this issue, clearly demonstrates that slow inbreeding maintains more genetic diversity than fast inbreeding and that the primary mechanism could be balancing selection. In their study, populations that took 19 generations, rather than one generation, to reach the same level of inbreeding maintained 10% higher levels of allelic richness and 25% higher levels of heterozygosity. The use of specifically chosen molecular markers not expected to be neutral makes this study especially noteworthy, as the study provides evidence concerning the mechanisms underlying the maintenance of genetic diversity in the face of inbreeding.     

Multilocus heterozygosity, parental relatedness and individual fitness components in a wild mountain goat, Oreamnos americanus population

Matings between relatives lead to a decrease in offspring genetic diversity which can reduce fitness, a phenomenon known as inbreeding depression. Because alpine ungulates generally live in small structured populations and often exhibit a polygynous mating system, they are susceptible to inbreeding. Here, we used marker-based measures of pairwise genetic relatedness and inbreeding to investigate the fitness consequences of matings between relatives in a long-term study population of mountain goats ( Oreamnos americanus ) at Caw Ridge, Alberta, Canada. We first assessed whether individuals avoided mating with kin by comparing actual and random mating pairs according to their estimated genetic relatedness, which was derived from 25 unlinked polymorphic microsatellite markers and reflected pedigree relatedness. We then examined whether individual multilocus heterozygosity H , used as a measure of inbreeding, was predicted by parental relatedness and associated with yearling survival and the annual probability of giving birth to a kid in adult females. Breeding pairs identified by genetic parentage analyses of offspring that survived to 1 year of age were less genetically related than expected under random matings. Parental relatedness was negatively correlated with offspring H , and more heterozygous yearlings had higher survival to 2 years of age. The probability of giving birth was not affected by H in adult females. Because kids that survived to yearling age were mainly produced by less genetically related parents, our results suggest that some individuals experienced inbreeding depression in early life. Future research will be required to quantify the levels of gene flow between different herds, and evaluate their effects on population genetic diversity and dynamics.     

Computer system for simulating population dynamic patterns of polygenes and mobile genetic elements upon truncation selection for a quantitative trait

A computer system was developed for simulation of population dynamics of interacting polygene patterns and mobile genetic elements (MGEs) under selection for a quantitative trait. The system is stochastic (Monte Carlo) and takes into account the main sources of random change in the patterns (recombinations, transpositions, excisions), genetic drift, and determined trends of selection and other genetic processes in a finite population. Using this model, it is possible to analyze the dynamics of many population parameters that cannot be experimentally estimated: frequencies of polygenic alleles, proportions of adaptive and random fixations, average heterozygosities of polygenes and MGEs, coefficient of inbreeding, heritability, etc. In addition, the model can be used to test various hypotheses on polygene-MGE interaction.     

Evaluation of major genetic loci contributing to inbreeding depression for survival and early growth in a selfed family of Pinus taeda

The magnitude of fitness effects at genetic loci causing inbreeding depression at various life stages has been an important question in plant evolution. We used genetic mapping in a selfed family of loblolly pine (Pinus taeda L.) to gain insights on inbreeding depression for early growth and viability. Two quantitative trait loci (QTLs) were identified that explain much of the phenotypic variation in height growth through age 3 and may account for more than 13% inbreeding depression in this family. One of these QTLs maps to the location of cad-nl, a lignin biosynthesis mutation. Both QTLs show evidence of overdominance, although evidence for true versus pseudo-overdominance is inconclusive. Evidence of directional dominance for height growth was noted throughout the genome, suggesting that additional loci may contribute to inbreeding depression. A chlorophyll-deficiency mutation, spf did not appear to be associated with growth effects, but had significant effects on survival through age 3. Previously identified embryonic viability loci had little or no overall effect on germination, survival, or growth. Our results challenge, at least in part, the prevailing hypothesis that inbreeding depression for growth is due to alleles of small effect. However, our data support predictions that loci affecting inbreeding depression are largely stage specific.     

采用微卫星标记分析10个双峰驼群体的遗传变异和群体间的遗传关系

为从分子水平上对我国双峰驼(Camelus bactrianus)群体的遗传多样性、群体间遗传关系、群体遗传分化及近交情况进行全面、系统地研究,为双峰驼种质资源保护和新品种培育提供基础数据,本文利用18对微卫星引物,分析了我国9个双峰驼群体和1个蒙古双峰驼群体的遗传多样性和遗传关系。结果显示:10个群体均具有较高的遗传多样性,共检测到242个等位基因,平均等位基因数为13.44,平均有效等位基因数为4.18,平均观察杂合度(Ho)为0.5528。10个群体间存在显著的遗传分化,有9.6%的遗传变异来自群体间,90.4%的遗传变异来自群体内部的个体间。聚类分析、主成分分析和群体遗传结构分析结果都表明10个群体被分成2个明显的分支,新疆4个群体单独聚为一类,剩下的6个群体聚为一类。这一结果可能与它们的地理分布和群体间的地理屏障有关。     

Ancient Demographics Determine the Effectiveness of Genetic Purging in Endangered Lizards

The purging of deleterious alleles has been hypothesized to mitigate inbreeding depression, but its effectiveness in endangered species remains debatable. To understand how deleterious alleles are purged during population contractions, we analyzed genomes of the endangered Chinese crocodile lizard (Shinisaurus crocodilurus), which is the only surviving species of its family and currently isolated into small populations. Population genomic analyses revealed four genetically distinct conservation units and sharp declines in both effective population size and genetic diversity. By comparing the relative genetic load across populations and conducting genomic simulations, we discovered that seriously deleterious alleles were effectively purged during population contractions in this relict species, although inbreeding generally enhanced the genetic burden. However, despite with the initial purging, our simulations also predicted that seriously deleterious alleles will gradually accumulate under prolonged bottlenecking. Therefore, we emphasize the importance of maintaining a minimum population capacity and increasing the functional genetic diversity in conservation efforts to preserve populations of the crocodile lizard and other endangered species.     

Strong spatial genetic structure in peripheral but not core populations of Sitka spruce [Picea sitchensis (Bong.) Carr.

We examined spatial genetic structure within eight populations of Sitka spruce classified as core or peripheral based on ecological niche, and continuous or disjunct based on species distribution. In each population, 200 trees were spatially mapped and genotyped for eight cDNA-based sequence tagged site (STS) codominant markers. Spatial autocorrelation was assessed by estimating p(ij), the average co-ancestry coefficient, between individuals within distance intervals. The distribution of alleles and genotypes within core populations was almost random, with nonsignificant co-ancestry values among trees as close as 50 m in core populations. In contrast, the distribution of alleles and genotypes within peripheral populations revealed an aggregation of similar multilocus genotypes, with co-ancestry values greater than 0.20 among trees up to 50 m apart and significant, positive values between trees up to 500 m. The relatively high density of reproductive adults in core populations may lead to highly overlapping seed shadows that limit development of spatial genetic structure. However, in peripheral populations with a lower density of adults, the distribution of alleles and genotypes was highly structured, likely due to offspring establishment near maternal trees and subsequent biparental inbreeding, as well as more recent population establishment at the leading edge of post-Pleistocene range expansion. Conserving genetic diversity in peripheral populations may require larger reserves for in situ conservation than required in core populations. These data on spatial genetic structure can be used to provide guidance for sampling strategies for both ex situ conservation and research collections.     

EFFECTIVENESS OF SELECTION IN REDUCING THE GENETIC LOAD IN POPULATIONS OF PEROMYSCUS POLIONOTUS DURING GENERATIONS OF INBREEDING

It has been hypothesized that natural selection reduces the “genetic load” of deleterious alleles from populations that inbreed during bottlenecks, thereby ameliorating impacts of future inbreeding. We tested the efficiency with which natural selection purges deleterious alleles from three subspecies of Peromyscus polionotus during 10 generations of laboratory inbreeding by monitoring pairing success, litter size, viability, and growth in 3604 litters produced from 3058 pairs. In P. p. subgriseus, there was no reduction across generations in inbreeding depression in any of the fitness components. Strongly deleterious recessive alleles may have been removed previously during episodes of local inbreeding in the wild, and the residual genetic load in this population was not further reduced by selection in the lab. In P. p. rhoadsi, four of seven fitness components did show a reduction of the genetic load with continued inbreeding. The average reduction in the genetic load was as expected if inbreeding depression in this population is caused by highly deleterious recessive alleles that are efficiently removed by selection. For P. p. leucocephalus a population that experiences periodic bottlenecks in the wild, the effect of further inbreeding in the laboratory was to exacerbate rather than reduce the genetic load. Recessive deleterious alleles may have been removed from this population during repeated bottlenecks in the wild; the population may be close to a threshold level of heterozygosity below which fitness declines rapidly. Thus, the effects of selection on inbreeding depression varied substantially among populations, perhaps due to different histories of inbreeding and selection.     

Pedigree and marker information requirements to monitor genetic variability

There are several measures available to describe the genetic variability of populations. The average inbreeding coefficient of a population based on pedigree information is a frequently chosen option. Due to the developments in molecular genetics it is also possible to calculate inbreeding coefficients based on genetic marker information. A simulation study was carried out involving ten sires and 50 dams. The animals were mated over a period of 20 discrete generations. The population size was kept constant. Different situations with regard to the level of polymorphism and initial allele frequencies and mating scheme (random mating, avoidance of full sib mating, avoidance of full sib and half sib mating) were considered. Pedigree inbreeding coefficients of the last generation using full pedigree or 10, 5 and 2 generations of the pedigree were calculated. Marker inbreeding coefficients based on different sets of microsatellite loci were also investigated. Under random mating, pedigree-inbreeding coefficients are clearly more closely related to true autozygosity (i.e., the actual proportion of loci with alleles identical by descent) than marker-inbreeding coefficients. If mating is not random, the demands on the quality and quantity of pedigree records increase. Greater attention must be paid to the correct parentage of the animals.     

Estimation of genetic purging under competitive conditions

Inbreeding depression for fitness traits is a key issue in evolutionary biology and conservation genetics. The magnitude of inbreeding depression, though, may critically depend on the efficiency of genetic purging, the elimination or recessive deleterious mutations by natural selection after they are exposed by inbreeding. However, the detection and quantification of genetic purging for nonlethal mutations is a rather difficult task. Here, we present two comprehensive sets of experiments with Drosophila aimed at detecting genetic purging in competitive conditions and quantifying its magnitude. We obtain, for the first time in competitive conditions, an estimate for the predictive parameter, the purging coefficient (d), that quantifies the magnitude of genetic purging, either against overall inbreeding depression (d ≈ 0.3), or against the component ascribed to nonlethal alleles (d_NL ≈ 0.2). We find that competitive fitness declines at a high rate when inbreeding increases in the absence of purging. However, in moderate size populations under competitive conditions, inbreeding depression need not be too dramatic in the medium to short term, as the efficiency of purging is also very high. Furthermore, we find that purging occurred under competitive conditions also reduced the inbreeding depression that is expressed in the absence of competition.     

遗传多样性与濒危植物保护生物学研究进展

尽管对于濒危物种的遗传学人们已经进行了大量研究,但是种群遗传学在植物保护中的实际地位尚存在很大争议。濒危物种的遗传多样性可能会由于遗传漂变、近交的作用而丧失;但这种丧失更可能是濒危的结果而不是濒危的起因。遗传多样性水平与物种生存力之间没有任何必然的联系。但植物种群遗传结构如果由于自交不亲和等位基因的丧失和与亲缘种杂交造成的遗传同化而发生改变,那么它对物种生存力会产生明显负作用。     

野古草种群克隆的遗传变异和遗传结构

用酶电泳法和同工酶分析对东北松嫩草原西北部野古草种群克隆遗传变异性和种群遗传结构做了探讨。讨论了遗传多样性、地理距离和遗传距离之间的关系、大种群和小种群的遗传变异性和种群间的基因流 ;种群间 ,包括大种群和小种群间基因流、遗传和地理距离对遗传多样性的影响、昆虫和风传粉、种群籽苗的补充、遗传多样性的发生和保持 ,自交不亲和性和无性繁殖及体细胞突变     

Mating animals by minimising the covariance between ancestral contributions generates less inbreeding without compromising genetic gain in breeding schemes with truncation selection

We reasoned that mating animals by minimising the covariance between ancestral contributions (MCAC mating) will generate less inbreeding and at least as much genetic gain as minimum-coancestry mating in breeding schemes where the animals are truncation-selected. We tested this hypothesis by stochastic simulation and compared the mating criteria in hierarchical and factorial breeding schemes, where the animals were selected based on breeding values predicted by animal-model BLUP. Random mating was included as a reference-mating criterion. We found that MCAC mating generated 4% to 8% less inbreeding than minimum-coancestry mating in the hierarchical and factorial breeding schemes without any loss in genetic gain. Moreover, it generated upto 28% less inbreeding and about 3% more genetic gain than random mating. The benefits of MCAC mating over minimum-coancestry mating are worthwhile because they can be achieved without extra costs or practical constraints. MCAC mating merely uses pedigree information to pair the animals more appropriately and is clearly a worthy alternative to minimum-coancestry mating and probably any other mating criterion. We believe, therefore, that MCAC mating should be used in breeding schemes where pedigree information is available.