Random Mating Research Articles

Matings Between Individuals with Similar Major Histocompatibility Complex (MHC) Improve Offspring Survival in the Rainbow Trout (Oncorhynchus mykiss)

The major histocompatibility complex (MHC) consists of genes involved in immune response and molecular discrimination between self and non-self. MHC genes are the most polymorphic in vertebrates. The origin and maintenance of polymorphism in MHC genes in populations is still unresolved. Mechanisms such as sexual selection and heterozygote advantage have been suggested as explanations for this high variability. In this study, a farmed population of rainbow trout (Oncorhynchus mykiss) characterized by the presence of specific MHC class IIB gene haplotypes at a frequency higher (30%) than that expected from random matings was investigated. Therefore, it was hypothesized that disassortative matings occur with an adaptive advantage for females, resulting in improved reproductive performance when mated with individuals with similar MHC haplotypes. Genetic analyses of the breeders were performed to define the MHC haplotypes and to perform specific matings. The effect of mating was evaluated by analyzing the survival rate of the offspring at various stages of incubation until swim-up. The reproductive performance of the offspring derived from specimens with similar haplotypes showed a better survival trend during the first life stages and reduced malformations. The results obtained are in contrast with the heterozygous advantage theory, therefore it was hypothesized, as for other salmonid species, the presence of a positive selection towards locally adapted MHC genes that promotes reproduction between genetically similar individuals.

Too big to purge: persistence of deleterious Mutations in Island populations of the European Barn Owl (Tyto alba).

A key aspect of assessing the risk of extinction/extirpation for a particular wild species or population is the status of inbreeding, but the origin of inbreeding and the current mutational load are also two crucial factors to consider when determining survival probability of a population. In this study, we used samples from 502 barn owls from continental and island populations across Europe, with the aim of quantifying and comparing the level of inbreeding between populations with differing demographic histories. In addition to comparing inbreeding status, we determined whether inbreeding is due to non-random mating or high co-ancestry within the population. We show that islands have higher levels of inbreeding than continental populations, and that this is mainly due to small effective population sizes rather than recent consanguineous mating. We assess the probability that a region is autozygous along the genome and show that this probability decreased as the number of genes present in that region increased. Finally, we looked for evidence of reduced selection efficiency and purging in island populations. Among island populations, we found an increase in numbers of both neutral and deleterious minor alleles, possibly as a result of drift and decreased selection efficiency but we found no evidence of purging.

Sexing animals using biometry: Intra-pair comparison is often superior to discriminant functions

In sexually monomorphic animal species it is difficult to sex unknown individuals. The most widely used method of sexing in those cases is discriminant analysis. In species that are socially monogamous and have biparental care, however, there exists another method which utilises the intra-pair difference in the trait used in sexing. Equations for calculating the fraction of wrongly sexed individuals using both methods are given and used to show that the latter method is more exact than discriminant analysis. The advantages and limits of both methods are compared. Field data from the kittiwake (Rissa tridactyla) are used to exemplify the intra-pair comparison method, and to test the assumptions underlying this method for this species. Among other things, it is shown that kittiwakes display random mating with respect to head+bill length. Sexing kittiwakes at Hornøya, northern Norway, by intra-pair differences in head+bill length gives correct results in 96% of the cases.

Phenotypic characteristics of successful parental pairs in white-tailed deer: evidence of non-random mating

Phenotypic characteristics of successful parental pairs in white-tailed deer: evidence of non-random mating

Recombination fraction in pre-recombinant inbred lines (PRERIL) - revisiting a century old problem in genetics

BackgroundTraditional recombinant inbred lines (RILs) are generated from repeated self-fertilization or brother-sister mating from the F1 hybrid of two inbred parents. Compared with the F2 population, RILs cumulate more crossovers between loci and thus increase the number of recombinants, resulting in an increased resolution of genetic mapping. Since they are inbred to the isogenic stage, another consequence of the heterozygosity reduction is the increased genetic variance and thus the increased power of QTL detection. Self-fertilization is the primary form of developing RILs in plants. Brother-sister mating is another way to develop RILs but in small laboratory animals. To ensure that the RILs have at least 98% of homozygosity, we need about seven generations of self-fertilization or 20 generations of brother-sister mating. Prior to homozygosity, these lines are called pre-recombinant inbred lines (PRERIL). Phenotypic values of traits in PRERILs are often collected but not used in QTL mapping. To perform QTL mapping in PRERILs, we need the recombination fraction between two markers at generation t for t < 7 (selfing) or t < 20 (brother-sister mating) so that the genotypes of QTL flanked by the markers can be inferred.ResultsIn this study, we developed formulas to calculate the recombination fractions of PRERILs at generation t in self-fertilization, brother-sister mating, and random mating. In contrast to existing works in this topic, we used computer code to construct the transition matrix to form the Markov chain of genotype array between consecutive generations, the so-called recurrent equations.ConclusionsWe provide R functions to calculate the recombination fraction using the newly developed recurrent equations of ordered genotype array. With the recurrent equations and the R code, users can perform QTL mapping in PRERILs. Substantial time and effort can be saved compared with QTL mapping in RILs.

Comparative microsatellite analysis of zeboid cattle with breeds of Bos taurus

Comparative genotyping of a population of zeboid cattle (Bos taurus × Bos indicus) and eight populations of B. taurus breeds, including six domestic (Нolmogorskaya, Yaroslavskaya, Red Gorbatovskaya, Kostromskaya, Tagil’skaya, Gray Ukrainian) and two transboundary European breeds (Holstein and Brown Swiss). A total of 562 individuals were examined. Based on the results of the STR analysis, it was found that all population samples of B. taurus were characterized by an average allelic diversity AR = 4.87–6.7 and a fairly high level of genetic variability HE = 0.68–0.76 with a slight predominance of random matings FIS = –0.1... 0.0. In zeboid cattle, the corresponding indicators were AR = 5.96, HE = 0.72 and FIS = –0.0278. At the same time, differences in the genetic structure of the B. taurus breeds under consideration were largely determined by population-demographic fluctuations, and the genetic and phenotypic heterogeneity detected in the population of zeboid cattle was determined by a decrease in the effect of artificial selection.

A new method for ecologists to estimate heterozygote excess and deficit for multi-locus gene families.

The fixation index, F IS, has been a staple measure to detect selection, or departures from random mating in populations. However, current Next Generation Sequencing (NGS) cannot easily estimate F IS, in multi-locus gene families that contain multiple loci having similar or identical arrays of variant sequences of ≥1 kilobase (kb), which differ at multiple positions. In these families, high-quality short-read NGS data typically identify variants, but not the genomic location, which is required to calculate F IS (based on locus-specific observed and expected heterozygosity). Thus, to assess assortative mating, or selection on heterozygotes, from NGS of multi-locus gene families, we need a method that does not require knowledge of which variants are alleles at which locus in the genome. We developed such a method. Like F IS, our novel measure, 1 H IS, is based on the principle that positive assortative mating, or selection against heterozygotes, and some other processes reduce within-individual variability relative to the population. We demonstrate high accuracy of 1 H IS on a wide range of simulated scenarios and two datasets from natural populations of penguins and dolphins. 1 H IS is important because multi-locus gene families are often involved in assortative mating or selection on heterozygotes. 1 H IS is particularly useful for multi-locus gene families, such as toll-like receptors, the major histocompatibility complex in animals, homeobox genes in fungi and self-incompatibility genes in plants.

Female‐biased population sex ratios caused by genetic rather than ecological mechanisms in dwarf willow (Salix herbacea L.)

Abstract Biased sex ratios among reproductive individuals are common in plants, but the underlying mechanisms, as well as the evolutionary consequences, are not well understood. The classical theory of Düsing and Fisher predicts an equal primary sex ratio at seed production, based on the selective advantage of the rare sex. Biased sex ratios among reproductive plants can arise from sexual dimorphism in survival and flowering. Sex ratio biases can also be present from the seed stage; in these cases, assumptions of Düsing's and Fisher's theory, for example, random mating or demographic equilibrium, are thought to be violated. We investigated mechanisms leading to female‐biased sex ratios in the arctic‐alpine dwarf willow Salix herbacea L. We studied sex ratios in three natural populations over 3 years as well as in 29 crosses (full‐sib families) under controlled conditions over four growth periods. We tested whether sex ratio was associated with habitat parameters (elevation and snowmelt time), or with germination, survival or flowering, and whether females and males differed in size or flowering that may cause observation bias. We detected a strong and consistent female bias, both in natural populations (sex ratio [proportion of females]: 0.71–0.82) and in our controlled experiment (overall sex ratio: 0.70–0‐72). Female bias became more pronounced with increasing elevation. Our data did not support sexual dimorphism in size or flowering. Family sex ratios varied largely (from 0.25 to 1), including many female‐biased families, unbiased families and two male‐biased families. Families with lower germination, seedling establishment, survival or flowering did not have stronger female bias, indicating that intrinsically higher survival or flowering in females does not explain overall female bias. Synthesis. Our results suggest that sex ratio bias in S. herbacea is already present in seeds and does not arise through intrinsic differences between sexes. Candidate mechanisms that can lead to both overall female bias and variation in sex ratio among families are meiotic drive or cyto‐nuclear interactions. The pioneer habit of Salix may lead to non‐equilibrium population dynamics that allow for the long‐term persistence of variable genetic sex ratio distortion systems that arise from genetic conflict.

Unifying quantification methods for sexual selection and assortative mating using information theory

Sexual selection plays a crucial role in modern evolutionary theory, offering valuable insight into evolutionary patterns and species diversity. Recently, a comprehensive definition of sexual selection has been proposed, defining it as any selection that arises from fitness differences associated with nonrandom success in the competition for access to gametes for fertilization. Previous research on discrete traits demonstrated that non-random mating can be effectively quantified using Jeffreys (or symmetrized Kullback-Leibler) divergence, capturing information acquired through mating influenced by mutual mating propensities instead of random occurrences. This novel theoretical framework allows for detecting and assessing the strength of sexual selection and assortative mating.In this study, we aim to achieve two primary objectives. Firstly, we demonstrate the seamless alignment of the previous theoretical development, rooted in information theory and mutual mating propensity, with the aforementioned definition of sexual selection. Secondly, we extend the theory to encompass quantitative traits. Our findings reveal that sexual selection and assortative mating can be quantified effectively for quantitative traits by measuring the information gain relative to the random mating pattern. The connection of the information indices of sexual selection with the classical measures of sexual selection is established.Additionally, if mating traits are normally distributed, the measure capturing the underlying information of assortative mating is a function of the square of the correlation coefficient, taking values within the non-negative real number set [0, +∞).It is worth noting that the same divergence measure captures information acquired through mating for both discrete and quantitative traits. This is interesting as it provides a common context and can help simplify the study of sexual selection patterns.

"Isolation by Gentes with Asymmetric Migration" shapes the genetic structure of the common cuckoo in China.

Amid coevolutionary arms races between brood parasitic birds and their diverse host species, the formation of host-specific races, or gentes, has drawn significant research focus. Nevertheless, numerous questions about gentes evolutionary patterns persist. Here, we investigated the potential for gentes evolution across multiple common cuckoo (Cuculus canorus) populations parasitizing diverse host species in China. Using maternal (mitochondrial and W-linked DNA) and biparental (autosomal and Z-linked DNA) markers, we found consistent clustering of cuckoo gentes (rather than geographical populations) into distinct clades in matrilineal gene trees, indicating robust differentiation. In contrast, biparental markers indicated intermixing of all gentes, suggesting asymmetric gene flow regardless of geography. Unlike the mitonuclear discordance commonly resulting from incomplete lineage sorting, adaptive introgression, or demographic disparities, the observed pattern in brood parasitic cuckoos might reflect biased host preferences between sexes. We hereby present the "Isolation by Gentes with Asymmetric Migration" model. According to this model, the maternal line differentiation of the common cuckoo in China is potentially driven by host preferences in females, whereas males maintained the integrity of the cuckoo species through random mating. To achieve this, cuckoo males could perform flexible migration among gentes or engage in early copulation with females before reaching the breeding sites, allowing female cuckoos to store sperm from various gentes. Future studies collecting additional samples from diverse cuckoo gentes with overlapping distribution and investigating the migratory and copulation patterns of each sex would enhance our understanding of sex-biased differentiation among cuckoo populations in China.

GENETIC INSIGHTS AND BREEDING IMPLICATIONS: ENHANCING COTTON YIELD AND QUALITY THROUGH BIPARENTAL SELECTION

This study was performed in Egypt's Sakha Agriculture Research Station during the seasons 2015–2018 to study the efficiency of biparental progenies derived from inter-population random mating in F2 generation in a cotton cross. Intercrossing is allowed in cotton breeding populations. Although the best lines may include harmful alleles, thus early segregating generation recombination and hybridization are required. The F2 generation of the cotton cross (Giza70 TNB1), which obtained from Agriculture Research Center, Egypt, consisted of five male and eight female plants, was used to test biparental progeny from random interpopulation mating. About 28 and 24 families in BIPS1 and BIPS2 had their original parents were examined. All genotypes were assessed for agricultural and fiber qualities. The mean of families (BIPs2) was higher than BIPs1 for all measured metrics except lint yield, percentage, and uniformity ratio. BIPS2 families had more genotypic coefficients of variation (GCV) for features than BIPS1. Intercrossing affected correlation coefficients of BIPS1 and BIPS2 genotypes. Seed cotton yield and lint index genotypic correlations became considerable. Seed cotton yield estimated by seed index and first fruiting node location were altered from negative to positive. Among them, No.5, No.7, No.8, No.18, and No.19 had large yields and early ripening, as shown by their components. The top five families chosen for fiber length had gain values of 3.373% to 8.961% and 5.919 to 7.781% for fiber strength. The No.18 family exhibited good seed cotton production and fiber length. Intermating and self-pollination (BIPS2) may utilize non-additive gene effects and accumulate trait-influencing alleles. Continuing to select and evaluate families based on their large-scale reproductive performance will enhance the likelihood of producing genotypes with desired features. In conclusion, this study underscores the utility of continued selection based on discerned genetic parameters, genotypic correlations, and observed gains in facilitating the ongoing improvement of cotton breeding programs. By providing valuable insights into the intricacies of genetic variability and trait associations, this research holds implications not only for the advancement of cotton breeding practices but also for the broader agricultural landscape on both national and global scales. Keywords: Biparental, selection efficiency, correlated response, hybridization, self-pollination

Population genetics assessment of two pocilloporid coral species from the northern red sea: Implications for urbanized reef sustainability

Understanding the genetic makeup of key coral species is vital for effective coral reef management, as heightened genetic diversity directly influences long-term survival and resilience against environmental changes. This study focused on two widespread Indo-Pacific branching corals, Pocillopora damicornis (referred as Pocillopora cf. damicornis (as identified only morphologically) and Seriatopora hystrix, by genotyping 222 and 195 colonies, respectively, from 10 sites in the northern Gulf of Eilat, Red Sea, using six and five microsatellite markers, respectively. Both species exhibited low observed heterozygosity (0.47 for P. cf. damicornis, 0.32 for S. hystrix) and similar expected heterozygosity (0.576 for P. cf. damicornis, 0.578 for S. hystrix). Pocillopora cf. damicornis showed minimal deviations from Hardy-Weinberg equilibrium (HWE) and low but positive F values, indicating high gene flow, while S. hystrix exhibited higher diversion from HWE and positive F values, suggesting isolation by distance and possible non-random mating or genetic drift. As the Gulf of Eilat undergoes rapid urbanization, this study highlights the anthropogenic impacts on the population genetics of key ecosystem engineering species and emphasizes the importance of managing genetics of Marine Protected Areas while implementing active coral reef restoration. The differences in reproductive traits between the two species (S. hystrix being a brooder, while P. cf. damicornis a broadcast spawner), underscore the need for sustainable population genetics management of the coral reefs for the future and resilience of the coral reef ecosystem of the northern Red Sea region.

A red flag: an experimental analysis of the function of pink colouration in males of Calopteryx haemorrhoidalis asturica (Odonata: Calopterygidae).

Males display phenotypic characteristics that may be associated with their quality, allowing non-random mating and post-copulatory female choice. In the damselfly Calopteryx haemorrhoidalis asturica, males have a conspicuous pink colouration in the underside of abdominal segments 8-10, which they exhibit during pre- and post-copulatory courtship. We hypothesized that this colouration functions to increase male mating success and/or to elicit females to oviposit. We estimated mating and oviposition success of 27 males, and on the following day, treated males had their segments 8-10 painted black and control males the seventh segment. We recorded the number of male-male fights and courtships, whether the courtship ended in copulation, and whether the female remained in the territory and laid eggs. Our results indicate that the mating success of male C. h. asturica was not significantly affected by the removal of the pink colouration of the abdominal tip, but this colouration clearly affected their success in enticing females to oviposit. Courtship frequency, fat content and muscle mass were positively correlated to male mating rate, and the number of aggressive encounters was negatively correlated. Our study yields experimental evidence for the function of pink colouration of male C. h. asturica, in the context of post-copulatory sexual selection.

Measuring the Efficiency of Purging by non-random Mating in Human Populations.

Human populations harbor a high concentration of deleterious genetic variants. Here, we tested the hypothesis that non-random mating practices affect the distribution of these variants, through exposure in the homozygous state, leading to their purging from the population gene pool. To do so, we produced whole-genome sequencing data for two pairs of Asian populations exhibiting different alliance rules and rates of inbreeding, but with similar effective population sizes. The results show that populations with higher rates of inbred matings do not purge deleterious variants more efficiently. Purging therefore has a low efficiency in human populations, and different mating practices lead to a similar mutational load.

Disentangling genetic diversity of Myotis septentrionalis: population structure, demographic history, and effective population size

Abstract Myotis septentrionalis (Northern Long-eared Bat) has recently suffered a &amp;gt;90% decline in population size in North America due to white-nose syndrome (WNS). We assessed genetic diversity, population structure, current effective population size, and demographic history of M. septentrionalis distributed across the United States to determine baseline levels pre-WNS. We analyzed RADseq data from 81 individuals from Kentucky, Louisiana, Michigan, Minnesota, North Carolina, Oklahoma, and Wisconsin. Additionally, we examined population genetic structure using discriminant analysis of principal components, fastStructure, and STRUCTURE. We then estimated effective population size and demographic history using fastsimcoal2. Similar levels of genetic diversity were found across all samples. We found no population genetic structure in the varied analyses from these contemporary samples. The best model for demographic history estimated a rapid population expansion followed by a slower expansion approximately 340,000 years ago. The vagility of M. septentrionalis, along with male dispersal and random mating, may provide a buffer against serious bottleneck effects stemming from rapid population declines due to WNS. This research provides a baseline for tracking and monitoring the influence of WNS on genetic diversity such as potential reduced diversity or increased population structuring in the future.

Population Dependent Two-Sex Branching Process with Random Mating and Overlapping Generations

Abstract This research focuses on stochastic modeling of the evolution over time of biological populations through branching processes. We introduce a new class of discrete time two-sex branching processes with random mating and overlapping generations. Mating and reproduction are considered to be influenced by the numbers of females and males existing in the population. This evolution over time with generational overlap is a novel research in two-sex branching process literature. We study general probabilistic properties and establish some limiting results of biological interest.

Population Genetics : A Review

Genetics is the study of genes and genetic variations alongwith the hereditary characteristics of an organism. Genetics is a central pillar of biology. It overlaps with other areas, such as: Agriculture, Medicine, Biotechnology. Genetics involves studying: Gene structure and function Gene variation and changes How genes affect health, appearance, and personality. Population genetics studies genetic variation within and among populations, based on the Hardy-Weinberg law, which remains constant in large populations with random mating and minimal mutation, selection, and migration.

A pollen selection system links self and interspecific incompatibility in the Brassicaceae.

Self-incompatibility and recurrent transitions to self-compatibility have shaped the extant mating systems underlying the nonrandom mating critical for speciation in angiosperms. Linkage between self-incompatibility and speciation is illustrated by the shared pollen rejection pathway between self-incompatibility and interspecific unilateral incompatibility (UI) in the Brassicaceae. However, the pollen discrimination system that activates this shared pathway for heterospecific pollen rejection remains unknown. Here we show that Stigma UI3.1, the genetically identified stigma determinant of UI in Arabidopsis lyrata × Arabidopsis arenosa crosses, encodes the S-locus-related glycoprotein 1 (SLR1). Heterologous expression of A. lyrata or Capsella grandiflora SLR1 confers on some Arabidopsis thaliana accessions the ability to discriminate against heterospecific pollen. Acquisition of this ability also requires a functional S-locus receptor kinase (SRK), whose ligand-induced dimerization activates the self-pollen rejection pathway in the stigma. SLR1 interacts with SRK and interferes with SRK homomer formation. We propose a pollen discrimination system based on competition between basal or ligand-induced SLR1-SRK and SRK-SRK complex formation. The resulting SRK homomer levels would be sensed by the common pollen rejection pathway, allowing discrimination among conspecific self- and cross-pollen as well as heterospecific pollen. Our results establish a mechanistic link at the pollen recognition phase between self-incompatibility and interspecific incompatibility.

Analysis of Endangered Andalusian Black Cattle (Negra Andaluza) Reveals Genetic Reservoir for Bovine Black Trunk.

This comprehensive study on the Andalusian Black cattle breed reveals a substantial population decline, with the average herd size decreasing significantly from 305.54 to 88.28 animals per herd. This decline is primarily attributed to agricultural changes and the introduction of foreign meat-focused breeds. The male-to-female ratio shift is noteworthy, with more cows than bulls, impacting selection intensity for both genders. Inbreeding levels, though relatively low historically (5.94%) and currently (7.23%), raise concerns as 37.08% historically and 48.82% currently of the animals exhibit inbreeding. Positive assortative mating is evident, reflected by the increasing non-random mating coefficient (α). Key ancestors play a crucial role in shaping genetic diversity, with one ancestor significantly influencing the current genetic pool and the top 10 ancestors contributing substantially. Breed maintains a conservation index of 2.75, indicating relatively high genetic diversity. Recent conservation efforts have led to an increase in registered animals. The Cañadas Reales, historical transhumance routes, may have contributed to genetic connections among provinces. Challenges include the historical bottleneck, demographic changes, and potential impacts from reproductive practices. The Andalusian Black breed's conservation necessitates ongoing efforts in genealogical registration, targeted breeding programs, and collaborative initiatives to address the observed demographic shifts and ensure sustainable genetic diversity.

Diversity of the Ghrelin Gene in Nigeria’s Fulani and Yoruba Ecotype Chickens

Ghrelin (GHRL) is a novel 28-amino acid gut-brain peptide linked to a gene associated with the regulation of growth hormones in birds. This study was carried out to investigate the polymorphism of the Ghrelin gene in Fulani and Yoruba ecotypes chickens in Nigeria. Blood samples were collected from seventy-eight (78) Nigerian indigenous chickens comprising of 41 Yoruba ecotype chickens and 37 Fulani ecotype chickens. Polymerase Chain Reaction-Restriction fragment length polymorphism (PCR-RFLP) method was used and the MboII restriction enzyme cut site 71 of the ghrelin and genetic structure were determined. Population structure was analyzed using allele and genotype frequencies, heterozygosity and genetic variation metrics. Two alleles (C and T) and three genotypes (CC, CT and TT) were observed. In the Yoruba Ecotype, the allele frequencies were C (0.34) and T (0.66) respectively while C (0.45) and T (0.55) were observed in the Fulani ecotype and the overall population was C (0.39) and T (0.61). The genotype frequencies obtained were; in the Yoruba ecotype, CC (0.10), CT (0.48), and TT (0.41) were observed. In the Fulani ecotype, CC (0.22), CT (0.45), and TT (0.32) were also observed, and in the overall population CC (0.15). CT (0.47) and TT (0.37) were observed. FIS values for the Yoruba ecotype (-0.0847) and Fulani ecotype (0.00702) reflects random mating and inbreeding respectively. The effective number of alleles indicates that the Fulani ecotype has more effective alleles compared to the Yoruba ecotype. These results suggest that the Yoruba ecotype may be at Hardy-Weinberg equilibrium, while Fulani ecotype deviates for the ghrelin locus. In summary, our results may open opportunities for genetic improvement in Nigerian indigenous chicken due to the polymorphic nature of the ghrelin gene.