Non-inbred Individuals Research Articles

Long-term exhaustion of the inbreeding load in Drosophila melanogaster

Inbreeding depression, the decline in fitness of inbred individuals, is a ubiquitous phenomenon of great relevance in evolutionary biology and in the fields of animal and plant breeding and conservation. Inbreeding depression is due to the expression of recessive deleterious alleles that are concealed in heterozygous state in noninbred individuals, the so-called inbreeding load. Genetic purging reduces inbreeding depression by removing these alleles when expressed in homozygosis due to inbreeding. It is generally thought that fast inbreeding (such as that generated by full-sib mating lines) removes only highly deleterious recessive alleles, while slow inbreeding can also remove mildly deleterious ones. However, a question remains regarding which proportion of the inbreeding load can be removed by purging under slow inbreeding in moderately large populations. We report results of two long-term slow inbreeding Drosophila experiments (125–234 generations), each using a large population and a number of derived lines with effective sizes about 1000 and 50, respectively. The inbreeding load was virtually exhausted after more than one hundred generations in large populations and between a few tens and over one hundred generations in the lines. This result is not expected from genetic drift alone, and is in agreement with the theoretical purging predictions. Computer simulations suggest that these results are consistent with a model of relatively few deleterious mutations of large homozygous effects and partially recessive gene action.

Consistent scaling of inbreeding depression in space and time in a house sparrow metapopulation

Inbreeding may increase the extinction risk of small populations. Yet, studies using modern genomic tools to investigate inbreeding depression in nature have been limited to single populations, and little is known about the dynamics of inbreeding depression in subdivided populations over time. Natural populations often experience different environmental conditions and differ in demographic history and genetic composition, characteristics that can affect the severity of inbreeding depression. We utilized extensive long-term data on more than 3,100 individuals from eight islands in an insular house sparrow metapopulation to examine the generality of inbreeding effects. Using genomic estimates of realized inbreeding, we discovered that inbred individuals had lower survival probabilities and produced fewer recruiting offspring than noninbred individuals. Inbreeding depression, measured as the decline in fitness-related traits per unit inbreeding, did not vary appreciably among populations or with time. As a consequence, populations with more resident inbreeding (due to their demographic history) paid a higher total fitness cost, evidenced by a larger variance in fitness explained by inbreeding within these populations. Our results are in contrast to the idea that effects of inbreeding generally depend on ecological factors and genetic differences among populations, and expand the understanding of inbreeding depression in natural subdivided populations.

Relatedness coefficients in pedigrees with inbred founders

We study an extension of the standard framework for pedigree analysis, in which we allow pedigree founders to be inbred. This solves a number of practical challenges in calculating coefficients of relatedness, including condensed identity coefficients. As a consequence we expand considerably the class of pedigrees for which such coefficients may be efficiently computed. An application of this is the modelling of background inbreeding as a continuous effect. We also use inbred founders to shed new light on constructibility of relatedness coefficients, i.e., the problem of finding a genealogy yielding a given set of coefficients. In particular, we show that any theoretically admissible coefficients for a pair of noninbred individuals can be produced by a finite pedigree with inbred founders. Coupled with our computational methods, implemented in the R package ribd, this allows for the first time computer analysis of general constructibility solutions, thus making them accessible for practical use.

Fast and accurate relatedness estimation from high-throughput sequencing data in the presence of inbreeding.

BackgroundThe estimation of relatedness between pairs of possibly inbred individuals from high-throughput sequencing (HTS) data has previously not been possible for samples where we cannot obtain reliable genotype calls, as in the case of low-coverage data.ResultsWe introduce ngsRelateV2, a major revision of ngsRelateV1, a program that originally allowed for estimation of relatedness from HTS data among non-inbred individuals only. The new revised version takes into account the possibility of individuals being inbred by estimating the 9 condensed Jacquard coefficients along with various other relatedness statistics. The program is threaded and scales linearly with the number of cores allocated to the process.ConclusionThe program is available as an open source C/C++ program under the GPL license and hosted at https://github.com/ANGSD/ngsRelate. To facilitate easy analysis, the program is able to work directly on the most commonly used container formats for raw sequence (BAM/CRAM) and summary data (VCF/BCF).

Inbreeding effects on in vitro embryo production traits in Guzerá cattle

Inbreeding has been associated with the impairment of reproductive performance in many cattle breeds. Although the usage of reproductive biotechnologies has been increasing in bovine populations, not much attention has been given to the impact of inbreeding over cow’s performance on artificial reproduction. The objective of this study was to estimate the impact of inbreeding on in vitro embryo production in a Guzerá breed population. The inbreeding coefficient (F), calculated as half of the co-ancestry of the individual’s parents, was used as an estimate of inbreeding. The inbreeding coefficients of the donor, sire (used on in vitro fertilization) and of the embryos were included, separately, in the proposed models either as classificatory or continuous variables (linear and quadratic effects). The percentage of non-inbred individuals (or embryos) and mean F of donors, embryos and sires were 29.38%; 35.76%; 42.86% and 1.98±2.68; 1.32±3.13; 2.08±2.79, respectively. Two different models were considered, one for oocyte production traits and other for embryo production traits. The increase of F of the donor significantly (P<0.05) impaired the number of viable oocytes (NOV), number of grade I oocytes (NGI) and number of cleaved embryos (NCLV). Moreover, the donor’s F influenced the percentage of grade I oocytes (PGI), percentage of viable embryos (PEMB) and percentage of cleaved embryos that turned into embryos (PCXE). No significant (P>0.05) effects were observed for the sire (father of the embryos) inbreeding coefficient over the traits analysed. Embryo’s F influenced (P<0.05) the number of viable embryos (NEMB), percentage of viable embryos (PEMB) and percentage of cleaved embryos that turn into embryos (PCXE). Results suggested that an increase in the inbreeding coefficient might impair the embryos ability to survive through challenges imposed by the in vitro environment. Submitting highly inbred Guzerá female donors to in vitro embryo production may, in the long-term, have negative implications on the number of embryos obtained per cow and increase the relative costs of the improvement programmes based on this technology. High levels of inbreeding should be avoided when selecting Guzerá female donors and planning in vitro fertilization mating.

Kin recognition in a butterfly: inferences about its heritability

Some animal species are able to recognise their relatives, cannibalising mostly non-kin individuals, as happens with the caterpillars of the butterfly Heliconius erato phyllis. Here, we established a breeding programme where adults had different coefficients of relatedness (r = 0 and r = 0.5; offspring, respectively with F = 0 and F = 0.25). The caterpillars cannibalised or did not cannibalise sibling eggs, which was used to make inferences on the kin recognition inheritance of non-cannibals, and to estimate its heritability. The parents had both cannibal and non-cannibal phenotypes; crosses were done for all combinations of these phenotypes, which were divided into outbred and inbred. Caterpillars were grown in the laboratory until the adult stage, and were classified as cannibal or non-cannibal after a test with three sibling eggs. The results showed that the mean number of non-cannibal siblings, those that recognise their kin, is larger in inbreds, above 60%, regardless of their parents’ behaviour. Among non-inbred individuals the mean frequency of non-cannibal siblings was around 38%; these differences were statistically significant. The heritability was estimated by four methods. For F = 0 it was around 0.24 ± 0.11, and for F = 0.25 it was around 0.20 ± 0.17. These results, taken together, were discussed in terms of a threshold character: above this threshold the expression of the non-cannibal phenotype is allowed. As for the low values for heritabilities, they were discussed in terms of the theory of traits relevant to both fitness and the resource allocation priority hypothesis.

Proteomic Characterization of Inbreeding-Related Cold Sensitivity in Drosophila melanogaster

Inbreeding depression is a widespread phenomenon of central importance to agriculture, medicine, conservation biology and evolutionary biology. Although the population genetic principles of inbreeding depression are well understood, we know little about its functional genomic causes. To provide insight into the molecular interplay between intrinsic stress responses, inbreeding depression and temperature tolerance, we performed a proteomic characterization of a well-defined conditional inbreeding effect in a single line of Drosophila melanogaster, which suffers from extreme cold sensitivity and lethality. We identified 48 differentially expressed proteins in a conditional lethal line as compared to two control lines. These proteins were enriched for proteins involved in hexose metabolism, in particular pyruvate metabolism, and many were found to be associated with lipid particles. These processes can be linked to known cold tolerance mechanisms, such as the production of cryoprotectants, membrane remodeling and the build-up of energy reserves. We checked mRNA-expression of seven genes with large differential protein expression. Although protein expression poorly correlated with gene expression, we found a single gene (CG18067) that, after cold shock, was upregulated in the conditional lethal line both at the mRNA and protein level. Expression of CG18067 also increased in control flies after cold shock, and has previously been linked to cold exposure and chill coma recovery time. Many differentially expressed proteins in our study appear to be involved in cold tolerance in non-inbred individuals. This suggest the conditional inbreeding effect to be caused by misregulation of physiological cold tolerance mechanisms.

Estimating relatedness with no prior specification of any genealogy: The role of the X-chromosome

Inferential studies on genetic relatedness fall into two broad approaches: (a) the genetic types of the individuals are used to compare the likelihood of their relatedness through specific genealogies; or (b) the genetic information is evaluated to infer the degree (or level) of relatedness between the individuals without specifying any pedigree. Approach (a) is used to compute statistics when the alternative pedigrees and/or samples are few (such as in the case of a standard paternity test, for example), while approach (b) is more general, and useful to bring into light cryptic, undisclosed or unspecified kinships (suited, for example, to seek for related individuals at mass disasters comparing recovered and reference samples). From a theoretical point of view, framework (a) is based on the complete set of identical-by-descent probabilities (three parameters for autosomes and a pair of non-inbred individuals), while (b) aims, in most cases, at the estimation of a single parameter: the coancestry coefficient θ, which is generally assumed as a coarser measure of genetic relatedness since it clusters pedigrees, such as “full-siblings” and “parent-child”, which are distinguishable through framework (a). In this work, under framework (b), we show that extending the standard estimation of the autosomal coancestry to X-chromosomal transmission can be a powerful approach to bring into light distant genealogies and to discern specific pedigrees, mainly if combined with the estimation of the autosomal counterpart. Indeed, for the latter purpose, the combined statistics for autosomes and X-chromosomal markers can be as powerful as that obtained with the, so far, unbeatable framework (a).

Inbreeding depression on production and reproduction traits of buffaloes from Brazil

The objective of this study was to evaluate the influence of inbreeding depression on traits of buffaloes from Brazil. Specifically, the traits studied were body weight at 205 and 365 days of age, average daily gain from birth to 205 days (ADG_205), average daily gain between 205 and 365 days (ADG205_365) in Mediterranean buffaloes, and milk yield, lactation length, age of first calving and calving intervals in Murrah buffaloes. Inbreeding effects on the traits were determined by fitting four regression models (linear, quadratic, exponential and Michaelis-Menten) about the errors generated by the animal model. The linear model was only significant (P < 0.05) for growth traits (exception of ADG205_365). The exponential and Michaelis-Menten models were significant (P < 0.01) for all the studied traits while the quadratic model was not significant (P > 0.05) for any of the traits. Weight at 205 and 365 days of age decreased 0.25 kg and 0.39 kg per 1% of increase in inbreeding, respectively. The inbred animals (F = 0.25) produced less milk than non-inbred individuals: 50.4 kg of milk. Moreover, calving interval increased 0.164 days per 1% of increase in inbreeding. Interestingly, inbreeding had a positive effect on age at first calving and lactation length, decreasing age of first calving and increasing lactation length.

Estimating coancestry from genotypes using a linear regression method

The estimation of the coancestry coefficient associated with a pair of individuals, given their genetic types, has been a matter of great theoretical and practical importance, namely in forensic kinship tests. Generally considered as a condensed measure of relatedness, it is quite often assumed that there is a loss of information when this measure is taken in consideration instead of Jacquard's identity-by-descent partitions. Nevertheless, considering non-inbred individuals, it can be proved that, excluding parent–child and full-siblings pedigrees, both measures are equivalent for genealogies that relate two individuals by exactly one path. In this work, the coancestry coefficient between two (not necessarily non-inbred) individuals is straightforwardly inferred from their genetic types through the probability of finding two identical alleles, each one randomly chosen from each individual, or, alternatively, through the expected homozygosity of their virtual offspring. The presented method is rooted in the algebraic expression for the probability of finding a homozygous individual in the population. It is shown that the coancestry coefficient of two individuals related by a given kinship can be mathematically modeled by a linear function depending on (a) the expected homozygosity of their virtual offspring, and (b) the average homozygosity in the population; the slope and the y-intercept of the straight line carrying information about the gene diversity of each database.

A general method to assess the utility of the X-chromosomal markers in kinship testing

In studies involving pedigree reconstruction and kinship estimation, it is acknowledged that some pedigrees have the same algebraic expressions for the joint genotypic probabilities and are, therefore, indistinguishable when considering only genetic information, no matter what the mode of transmission considered. Indeed, although standard forensic practice considers solely unlinked autosomal markers, the existence of pedigrees with the referred theoretical property (that are then said to belong to the same kinship class) is possible when considering any kind of genetic transmission. The research on genetic relatedness has always been linked to the root concept of identity-by-descent (IBD). However, although the basic theoretical core for autosomal transmission has been long formalised, a general method allowing the decision if two pedigrees linking two non-inbred individuals are distinguishable using unlinked autosomal markers along with the respective IBD partitions (and consequently the algebraic expressions for the joint genotypic probabilities) was only recently published.In this work X-chromosomal transmission will be at stake, considering that the analytical framework for X-chromosomal markers has been recently established and the importance of X-chromosome markers for these questions has been steadily growing, particularly in forensics, as a tool both to complement the information given by autosomes in complex kinship testing cases and to differentiate pedigrees belonging to the same autosomal kinship class. Therefore, here it will be presented a formal and mathematically well supported framework where a general counting rule is given, allowing a secure and expeditious decision on the usefulness of typing (unlinked) X-chromosomal markers on pairwise kinship testing involving two non-inbred individuals. Moreover the counting rule now presented allows the derivation of algebraic expressions for the joint genotypic probabilities associated with any pedigree.

Variation in actual relationship as a consequence of Mendelian sampling and linkage.

Although the expected relationship or proportion of genome shared by pairs of relatives can be obtained from their pedigrees, the actual quantities deviate as a consequence of Mendelian sampling and depend on the number of chromosomes and map length. Formulae have been published previously for the variance of actual relationship for a number of specific types of relatives but no general formula for non-inbred individuals is available. We provide here a unified framework that enables the variances for distant relatives to be easily computed, showing, for example, how the variance of sharing for great grandparent-great grandchild, great uncle-great nephew, half uncle-nephew and first cousins differ, even though they have the same expected relationship. Results are extended in order to include differences in map length between sexes, no recombination in males and sex linkage. We derive the magnitude of skew in the proportion shared, showing the skew becomes increasingly large the more distant the relationship. The results obtained for variation in actual relationship apply directly to the variation in actual inbreeding as both are functions of genomic coancestry, and we show how to partition the variation in actual inbreeding between and within families. Although the variance of actual relationship falls as individuals become more distant, its coefficient of variation rises, and so, exacerbated by the skewness, it becomes increasingly difficult to distinguish different pedigree relationships from the actual fraction of the genome shared.

X-chromosome markers in kinship testing: A generalisation of the IBD approach identifying situations where their contribution is crucial

The standard practice of forensic kinship evaluation uses unlinked autosomal markers. However, X-chromosome markers have recently gained recognition as a powerful tool to complement the information provided by autosomes, particularly in complex cases. In this paper, the X-chromosome mode of transmission is addressed in the theoretical identity-by-descent framework. Formulas for the joint genotypic probabilities considering various pedigrees relating two inbred and/or non-inbred individuals are derived. Finally, the importance of X-chromosome markers is highlighted by the fact that, in addition to complementing the autosomal information, X-chromosome transmission allows differential weighting of certain hypotheses regarding pedigrees belonging to the same autosomal class, i.e., pedigrees that are indistinguishable by the use of unlinked autosomal markers. Illustrative examples of common kinship testing are shown.

General Derivation of the Sets of Pedigrees with the Same Kinship Coefficients

Quantification of kinships between two individuals using unlinked autosomal markers rests upon the identity-by-descent (IBD) probabilities among their four alleles at a locus because they determine the algebraic expressions of the joint genotypic probabilities. Nevertheless, some pedigrees share the same IBD probabilities and are therefore indistinguishable using those markers. Examples of these pedigrees were previously described, such as the case of half-siblings, grandparent-grandchild and avuncular, but a general analysis has not been attempted. The aim of this study is to present a systematic and mathematically supported framework where considering unlinked autosomal markers complete sets of indistinguishable pedigrees linking two non-inbred individuals are generally derived. In our work, complete sets of pedigrees with the same IBD partitions are formally established and mathematically treated, considering kinships linking any pair of non-inbred individuals, whether they are related just maternally or paternally, or both. Moreover, general expressions for IBD partitions, and consequently for joint genotypic probabilities, are derived considering a simple counting rule based on two ‘atom’ pedigrees: parent-child and full-siblings. Besides the theoretical formalization of the problem, the developed framework has potential applications in forensics as well as in breeding strategies design and in conservation studies.

Quantitative Genetics of Inbreeding in a Synthetic Maize Population

The average effects of inbreeding depression have been measured extensively in maize (Zea mays L.), but the influence of inbreeding on genetic variance has not been well studied. Two hundred random S1, S2, S3, and S4 lines were developed from the BS13(S)C0 population by single-seed descent and a set of 200 related half-sib families were developed from the S1 lines. The lines and half-sib families were evaluated in replicated yield trials for six agronomic characters. Under a purely additive model, the expected variance among inbred individuals is exactly twice the variance of noninbred individuals. The observed variance of inbred individuals in our study was 1.18 times the variance of noninbred individuals or less for five of six traits studied. By contrast, variance of dominance deviations of inbred individuals ranged from 1.6 to 3.3 times the variance of dominance deviations of noninbred individuals for five of six traits studied. A negative covariance between dominance deviations and breeding values in inbred individuals was found for all six traits. An estimator of the degree of dominance for arbitrary allele frequencies was developed. The estimated average degree of dominance in BS13(S)C0 ranged from 1.28 to 2.76, corresponding to overdominance or pseudo-overdominance. Our results suggested that some regions of linked genes have large effects on inbreeding depression in this population.

Variables influencing survival in four generations of captive-born muskoxen

Since 1967, four generations of muskoxen have been born in captivity in Alaska (399 live births, 18 abortions and 47 stillbirths), all derived from 20 females and 8 males captured on Nunivak Island. Analysis of juvenile survival was accomplished by dividing individuals into 7 classes (not born live, born live but not surviving 48 hours, survived 48 hours but &amp;lt; 1 week, survived 1 week but &amp;lt; 1 month, survived 1 month but &amp;lt; 6 months, survived 6 months but &amp;lt; 2 years, survived 2 years). Males were more frequent among live born calves (219:178, P=0.05), but greater numbers of females survived to 2 years (62:86, P&amp;lt;0.01). Birthweight (X=9.75 kg, N=155) did not differ between sexes nor did it significantly influence survival. Of 463 individuals, 131 showed some inbreeding but no coefficients of inbreeding exceeded 0.25 and most were less than 0.13. Analysis of variance (Kruskal-Wallis) showed a significant (P&amp;lt;0.05) difference between survival of inbred and non-inbred individuals. Chi-squared tests showed a greater proportion of non-inbred calves surviving to 2 years (P&amp;lt;0.05) but no significant differences in perinatal mortality. Offspring of the Nunivak Island cows survived significantly (P&amp;lt;.01) longer than those whose mothers were born in captivity, even when only non-inbred calves were compared.

A theory of natural selection incorporating interaction among individuals. III. Use of random groups of inbred individuals

The present series of studies attempts to accommodate interaction among individuals in evolutionary theory. The interaction phenomenon is characterized by two dimensions (direct and associate) of gene activity. For optimal selection results, a balance between the two dimensions must occur. In the first paper of the series, it was shown that random interactions resulted in an unbalanced selection response in that the direct, but not associate, effects were included in the expression for gene frequency change. The next three papers of the series (II, III and IV) were designed to determine whether or not selection with life-history models that involved non-random interactions would be useful in ameliorating the problem of selection balance. In the present study, non-randomness is generated by restricting interactions to inbred individuals. It is demonstrated that this form of non-random gene association within interacting genotypes does not improve selection balance. Thus restricting interaction to groups of inbred individuals does not result in the introduction of associate effects into the expression for gene frequency change. It is shown that inbreeding in the base population merely accelerates the unbalanced response normally occurring when selection operates on random, non-inbred individuals.