Extreme Inbreeding Research Articles

Genomic signatures of inbreeding and mutation load in tree ferns.

Ferns (Pteridophyta), as the second largest group of vascular plants, play important roles in ecosystem functioning. Homosporous ferns exhibit a remarkable range of mating systems, from extreme inbreeding to obligate outcrossing, which may have significant evolutionary and ecological implications. Despite their significance, the impact of genome-wide inbreeding on genetic diversity and mutation load within the fern lineage remain largely unexplored. In this study, we utilized whole-genome sequencing to investigate the genomic signatures of inbreeding and genetic load in three Alsophila tree fern species. Our analysis revealed extremely high inbreeding in A. spinulosa, in contrast to the predominantly outcrossing observed in A. costularis and A. latebrosa. This difference likely reflects divergent mating systems and demographic histories. Consistent with its extreme inbreeding propensity, A. spinulosa exhibits reduced genetic diversity and a pronounced decline in effective population size. Comparison of genetic load revealed an overall reduction in deleterious mutations in the highly inbred A. spinulosa, highlighting that long-term inbreeding may have contributed to the purging of strongly deleterious mutations, thereby prolonging the survival of A. spinulosa. Despite this, however, A. spinulosa carries a substantive realized genetic load that may potentially instigate future fitness decline. Our findings illuminate the complex evolutionary interplay between inbreeding and mutation load in homosporous ferns, yielding insights with important implications for the conservation and management of these species.

The role of inbreeding depression on productive performance in the Italian Holstein breed.

Inbreeding depression has become an urgent issue in cosmopolitan breeds where the massive genetic progress achieved in the latest generations is counterbalanced by a dramatic loss of genetic diversity causing increased health issues. Thus, the aim of this study was to estimate inbreeding depression on productive traits in Holstein dairy cattle. More precisely, we aimed to i) determine the level of inbreeding in 27,735 Italian Holstein dairy cows using pedigree and genotype data, ii) quantify the effect of inbreeding on 305-d in milk yield (MY; kg), fat yield (FY; kg), and protein yield (PY; kg) based on different statistical approaches, iii) determine if recent inbreeding has a more harmful impact than ancestral ones, and iv) quantify chromosomal homozygosity effect on productive traits. Quality control was performed on the autosomal chromosomes resulting in a final dataset of 84,443 single nucleotide polymorphisms. Four statistical models were used to evaluate the presence of inbreeding depression, which included linear regression analysis and division of FPED and FROH into percentile classes. Moreover, FROH was partitioned into i) length classes to assess the role of recent and ancestral inbreeding and ii) chromosome-specific contributions (FROH-CHR). Results evidenced that inbreeding negatively impacted the productive performance of Italian Holstein Friesian cows. However, differences between the estimated FPED and FROH coefficients resulted in different estimates of inbreeding depression. For instance, a 1% increase in FPED and FROH was associated with a decrease in MY of about 44 and 61 kg (P < 0.01). Further, when considering the extreme inbreeding percentile classes moving from the 5th lowest to the 95th highest, there was a reduction of -263 kg and -561 kg per lactation for FPED and FROH. Increased inbreeding, estimated by FPED and FROH, had also a negative effect on PY and FY, either fit as a regressor or percentile classes. When evaluating the impact of inbreeding based on runs of homozygosity (ROH) length classes, longer ROH (over 8 Mb) had a negative effect in all traits, indicating that recent inbreeding might be more harmful than the ancestral one. Finally, results within chromosome homozygosity highlighted specific chromosomes with a more deleterious effect on productive traits.

Transposable elements maintain genome-wide heterozygosity in inbred populations

Elevated levels of inbreeding increase the risk of inbreeding depression and extinction, yet many inbred species are widespread, suggesting that inbreeding has little impact on evolutionary potential. Here, we explore the potential for transposable elements (TEs) to maintain genetic variation in functional genomic regions under extreme inbreeding. Capitalizing on the mixed mating system of Arabidopsis lyrata, we assess genome-wide heterozygosity and signatures of selection at single nucleotide polymorphisms near transposable elements across an inbreeding gradient. Under intense inbreeding, we find systematically elevated heterozygosity downstream of several TE superfamilies, associated with signatures of balancing selection. In addition, we demonstrate increased heterozygosity in stress-responsive genes that consistently occur downstream of TEs. We finally reveal that TE superfamilies are associated with specific signatures of selection that are reproducible across independent evolutionary lineages of A. lyrata. Together, our study provides an important hypothesis for the success of self-fertilizing species.

Relationship between body size and sexual size dimorphism in syringophilid quill mites

A positive relationship of body size and sexual size dimorphism (males’ size relative to females), called Rensch’s rule, is often observed in comparisons within non-parasitic taxa. However, this allometric relationship has rarely been tested in comparisons across closely related parasite species. Since male sexual rivalry is often regarded as the main cause of this phenomenon, the present study tests this rule in a taxon where sexual selection is almost totally absent in males. Body size data of (non-physogastric) female and male quill mites (Acari: Syringophilidae) were gathered from the literature to investigate this relationship. The data set consisted of 113 species representing 8 genera. For the data set as a whole, increasing body size came together with decreasing relative body size of males (relative to females), a phenomenon known as converse Rensch’s rule. Repeating the same analysis for the 8 genera separately, similar patterns were found in 4 significant and 3 non-significant cases. There was a significant tendency to comply with Rensch’s rule only in one genus, the Neoaulonastus. Thus, converse Rensch’s rule is the primary trend in syringophilid quill mites that appears repeatedly and independently in several genera. This phenomenon is probably caused by their extreme inbreeding, which strongly reduces sexual competition among males in this taxon.

A new method to reconstruct the direction of parent-offspring duo relationships using SNP array data and its demonstration on ancient and modern cultivars in the outcrossing species malus × domestica.

Unordered parent-offspring (PO) relationships are an outstanding issue in pedigree reconstruction studies. Resolution of the order of these relationships would expand the results, conclusions, and usefulness of such studies; however, no such PO order resolution (POR) tests currently exist. This study describes two such tests, demonstrated using SNP array data in the outcrossing species apple (Malus × domestica) on a PO relationship of known order (‘Keepsake’ as a parent of ‘Honeycrisp’) and two PO relationships previously ordered only via provenance information. The first test, POR-1, tests whether some of the extended haplotypes deduced from homozygous SNP calls from one individual in an unordered PO duo are composed of recombinant haplotypes from accurately phased SNP genotypes from the second individual. If so, the first individual would be the offspring of the second individual, otherwise the opposite relationship would be present. The second test, POR-2, does not require phased SNP genotypes and uses similar logic as the POR-1 test, albeit in a different approach. The POR-1 and POR-2 tests determined the correct relationship between ‘Keepsake’ and ‘Honeycrisp’. The POR-2 test confirmed ‘Reinette Franche’ as a parent of ‘Nonpareil’ and ‘Brabant Bellefleur’ as a parent of ‘Court Pendu Plat’. The latter finding conflicted with the recorded provenance information, demonstrating the need for these tests. The successful demonstration of these tests suggests they can add insights to future pedigree reconstruction studies, though caveats, like extreme inbreeding or selfing, would need to be considered where relevant.

Genome-wide single nucleotide polymorphism array and whole-genome sequencing reveal the inbreeding progression of Banna minipig inbred line.

Inbred pigs are promising animal models for biomedical research and xenotransplantation. Established in 1980, the Banna minipig inbred (BMI) line originated from a sow and its own male offspring. It was selected from a small backcountry minority Lahu village, where records show that no other pig breed has ever been introduced. During the inbreeding process, we perfomed extreme inbreeding over 23 consecutive generations using full-sibling or parent-offspring mating. In order to investigate the inbreeding effects in BMI pigs across generations over the past 40 years, in this study we conducted a genome-wide SNP genotyping of the last 10 generations, representing generations 14-23. In total, we genotyped 57,746 SNPs, corresponding to an average decrease in heterozygosity rate of 0.0078 per generation. Furthermore, we were only able to identify 18,216 polymorphic loci with a MAF larger than 0.05, which is substantially lower than the values in previous reports on other pig breeds. In addition, we sequenced the genome of the first pig in the twenty-third generation (inbreeding coefficient 99.28%) to an average coverage of 12.4× to evaluate at the genome level the impact of advanced inbreeding. ROH analysis indicates that BMI pigs have longer ROHs than Wuzhishan and Duroc pigs. Those long ROH regions in BMI pigs are enriched for distinct functions compared with the highly polymorphic regions. Our study reveals a genome-wide allele diversity loss during the progress of inbreeding in BMI pigs and characterizes ROH and polymorphic regions as a result of inbreeding. Overall, our results indicate the successful establishment of the BMI line, which paves the way for further in-depth studies.

An algorithm to represent inbreeding trees

Recent work has proven the existence of extreme inbreeding in a European ancestry sample taken from the contemporary UK population (Yengo et al., 2019). This result brings our attention again to a math problem related to inbreeding family trees and diversity. Groups with a finite number of individuals could give a variety of genetic relationships. In previous works (Caruso and Jarne, 2015; Caruso and Jarne, 2014; Jarne and Caruso, 2019), we have addressed the issue of building inbreeding trees for biparental reproduction using Markovian models. Here, we extend these studies by presenting an algorithm to generate and represent inbreeding trees with no overlapping generations. We explicitly assume a two-gender reproductory scheme, and we pay particular attention to the links between nodes. We show that even for a simple case with a relatively small number of nodes in the tree, there are a large number of possible ways to rearrange the links between generations. We present an open-source python code to generate the tree graph, the adjacency matrix, and the histogram of the links for each different tree representation. We show how this mapping reflects the difference between tree realizations, and how valuable information may be extracted upon inspection of these matrices. The algorithm includes a feature to average several tree realizations, obtain the connectivity distribution, and calculate the mean value and standard deviation. We used this feature to compare trees with a different number of generations and nodes. The code presented here, available in Git-Hub, may be easily modified to be applied to other areas of interest involving connections between individuals, extend the study to add more characteristics of the different nodes, etc.

Extensive hybridization and past introgression between divergent lineages in a quasi-clonal hermaphroditic fish: Ramifications for species concepts and taxonomy.

Extreme inbreeding is expected to reduce the incidence of hybridization, serving as a prezygotic barrier. Mangrove rivulus is a small killifish that reproduces predominantly by self-fertilization, producing highly homozygous lines throughout its geographic range. The Bahamas and Caribbean are inhabited by two highly diverged phylogeographic lineages of mangrove rivulus, Kryptolebias marmoratus and a 'Central clade' closely related to K.hermaphroditus from Brazil. The two lineages are largely allopatric, but recently were found in syntopy on San Salvador, Bahamas, where a single hybrid was reported. To better characterize the degree of hybridization and the possibility of secondary introgression, here we conducted a detailed genetic analysis of the contact zone on San Salvador. Two mixed populations were identified, one of which contained sexually mature hybrids. The distribution of heterozygosity at diagnostic microsatellite loci in hybrids showed that one of these hybrids was an immediate offspring from the K.marmoratus x Central clade cross, whereas the remaining five hybrids were products of reproduction by self-fertilization for 1-3 generations following the initial cross. Two hybrids had mitochondrial haplotypes of K.marmoratus and the remaining four hybrids had a haplotype of the Central clade, indicating that crosses go in both directions. In hybrids, alleles of parental lineages were represented in equal proportions suggesting lack of recent backcrossing to either of the parental lineages. However, sympatric populations of two lineages were less diverged than allopatric populations, consistent with introgression. Results are discussed in terms of applicability of the biological species concept for isogenic, effectively clonal, organisms.

‘Extreme inbreeding’ revealed by massive human-genome survey

‘Extreme inbreeding’ revealed by massive human-genome survey

Extreme inbreeding in a European ancestry sample from the contemporary UK population

In most human societies, there are taboos and laws banning mating between first- and second-degree relatives, but actual prevalence and effects on health and fitness are poorly quantified. Here, we leverage a large observational study of ~450,000 participants of European ancestry from the UK Biobank (UKB) to quantify extreme inbreeding (EI) and its consequences. We use genotyped SNPs to detect large runs of homozygosity (ROH) and call EI when >10% of an individual’s genome comprise ROHs. We estimate a prevalence of EI of ~0.03%, i.e., ~1/3652. EI cases have phenotypic means between 0.3 and 0.7 standard deviation below the population mean for 7 traits, including stature and cognitive ability, consistent with inbreeding depression estimated from individuals with low levels of inbreeding. Our study provides DNA-based quantification of the prevalence of EI in a European ancestry sample from the UK and measures its effects on health and fitness traits.

Development of Microsatellites for Population Genetic Analyses of the Granulate Ambrosia Beetle (Coleoptera: Curculionidae).

Limited male dispersal and local mating in ambrosia beetles are expected to result in extreme inbreeding and highly structured populations. In this study, we developed microsatellite markers for the granulate ambrosia beetle, Xylosandrus crassiusculus (Motschulsky), for use in future studies into population and family structure of this invasive pest species. We employed de novo next-generation sequencing to generate whole genome shotgun sequences for the characterization of microsatellite loci. Approximately 6% of the 84,024 contigs generated from Hi-Seq Illumina 2x250bp sequencing contained microsatellites with at least four repeats of di-, tri-, tetra-, penta-, and hexamers. Primers were synthesized for 40 microsatellite loci with trimer repeat units. Twenty-four primer pairs yielded consistent PCR products of unique loci and were validated for population genetic application using three sample groups each containing 20 X. crassiusculus individuals from Mississippi. Thirteen loci were found to be polymorphic with up to five alleles per population. The two beetle sample groups from Pearl River County (Poplarville and McNeill) belonged genetically to the same population. The population from Lamar County (Purvis) was genetically distinct, separated by a moderate genetic distance (FST = 0.11) and five unique alleles (with >5% frequency). Consistent with the perceived mating structure (incest of females with flightless males), the populations showed homozygote excess at most loci, as indicated by the coefficients of inbreeding (FIT = 0.45 and FIS = 0.37) and high mean relatedness among individuals (r = 0.15).

Seasonal cycle of inbreeding and recombination of the parasitic mite Varroa destructor in honeybee colonies and its implications for the selection of acaricide resistance

Varroa destructor is the most devastating parasite of the Western honeybee, Apis mellifera. In the light of the arm race opposing the host and its parasite, the population dynamics and genetic diversity of these organisms are key parameters. However, the life cycle of V. destructor is characterized by extreme inbreeding due to full sibling mating in the host brood cells. We here present an equation reflecting the evolution of inbreeding in such a clonal system, and compare our predictions with empirical data based on the analysis of seven microsatellite markers. This comparison revealed that the mites perform essentially incestuous mating in the beginning of the brood season. However, this pattern changes with the development of mite infestation. Despite the fact that the overall level of genetic diversity of the mites remained low through the season, multiple inbred lineages were identified in the mites we sampled in June. As a response to the decrease of brood availability and the increase of the parasite population in parallel in the colonies, these lineages recombined towards the end of the season as mites co-infest brood cells. Our results suggest that the ratio of the number of mite per brood cell in the colony determines the genetic structure of the populations of V. destructor. This intracolonial population dynamics has great relevance for the selection of acaricide resistance in V. destructor. If chemical treatments occur before the recombination phase, inbreeding will greatly enhance the fixation of resistance alleles at the colony level.

Sex and the Single Gametophyte: Revising the Homosporous Vascular Plant Life Cycle in Light of Contemporary Research

Homosporous vascular plants are typically depicted as extreme inbreeders, with bisexual gametophytes that produce strictly homozygous sporophytes. This view is promulgated in textbook life cycles despite ample evidence that natural populations of most species regularly outcross. We review research on a variety of mechanisms, including genetic load, asynchronous production of eggs and sperm, and pheromonal control of gamete production, that actively promote heterozygosity in ferns and lycophytes. Evolution of the land plants cannot be reconstructed without accurate depictions of the unique life cycle that has helped make ferns the second most diverse lineage of vascular plants on Earth. With revised illustrations and definitions, we provide scientists, educators, and students with a contemporary understanding of fern and lycophyte reproduction, revealing them as evolutionarily dynamic and exploiting a wide range of mating systems.

Quality of the Exotic Parasitoid Cotesia flavipes (Hymenoptera: Braconidae) Does Not Show Deleterious Effects after Inbreeding for 10 Generations.

Although the parasitoid Cotesia flavipes (Cameron) has proven effective in controlling sugarcane borer Diatraea saccharalis (Fabricius) for many years, concern has arisen over the quality of individuals produced at large scales. The parasitoid has been reared in laboratories in Brazil for more than 40 years, with no new introductions of new populations during that period. Since the quality of the parasitoids was not verified at the time of the species' introduction in Brazil, we do not know if there has been any reduction in quality so far. However, it is possible to determine whether the parasitoid could reduce in quality in future generations. Thus, the objective of this research was to assess the quality of these insects over 10 generations and look for evidence of any loss in quality. We used two populations: one from a biofactory that has been maintained in the laboratory for over 40 years, and an inbred laboratory population. Both were bred, and compared for 10 generations. We wanted to determine what happened to the quality of the parasitoid after 10 generations in an extreme inbreeding situation. To assure inbreeding, newly emerged females were forced to mate with a sibling. Individual females were then allowed to parasitize larvae of D. saccharalis. We performed evaluations for each generation until the tenth generation, and recorded the sex ratio, percentage emergence, number of offspring/females, and longevity of both males and females. Results of the measurements of biological characteristics demonstrated random significant differences between populations; best results were obtained intermittently for both the biofactory population and the inbred population. No significant differences across generations for the same population were observed. Thus, rearing of a C. flavipes population subjected to inbreeding for 10 generations was not sufficient to reveal any deleterious effects of inbreeding.

On the widespread capacity for, and functional significance of, extreme inbreeding in ferns.

Homosporous vascular plants utilize three different mating systems, one of which, gametophytic selfing, is an extreme form of inbreeding only possible in homosporous groups. This mating system results in complete homozygosity in all progeny and has important evolutionary and ecological implications. Ferns are the largest group of homosporous land plants, and the significance of extreme inbreeding for fern evolution has been a subject of debate for decades. We cultured gametophytes in the laboratory and quantified the relative frequencies of sporophyte production from isolated and paired gametophytes, and examined associations between breeding systems and several ecological and evolutionary traits. The majority of fern species studied show a capacity for gametophytic selfing, producing sporophytes from both isolated and paired gametophytes. While we did not follow sporophytes to maturity to investigate potential detrimental effects of homozygosity at later developmental stages, our results suggest that gametophytic selfing may have greater significance for fern evolution and diversification than has previously been realized. We present evidence from the largest study of mating behavior in ferns to date that the capacity for extreme inbreeding is prevalent in this lineage, and we discuss its implications and relevance and make recommendations for future studies of fern mating systems.

Unexpected positive and negative effects of continuing inbreeding in one of the world's most inbred wild animals.

Inbreeding depression, the reduced fitness of offspring of related individuals, is a central theme in evolutionary biology. Inbreeding effects are influenced by the genetic makeup of a population, which is driven by any history of genetic bottlenecks and genetic drift. The Chatham Island black robin represents a case of extreme inbreeding following two severe population bottlenecks. We tested whether inbreeding measured by a 20-year pedigree predicted variation in fitness among individuals, despite the high mean level of inbreeding and low genetic diversity in this species. We found that paternal and maternal inbreeding reduced fledgling survival and individual inbreeding reduced juvenile survival, indicating that inbreeding depression affects even this highly inbred population. Close inbreeding also reduced survival for fledglings with less-inbred mothers, but unexpectedly improved survival for fledglings with highly inbred mothers. This counterintuitive interaction could not be explained by various potentially confounding variables. We propose a genetic mechanism, whereby a highly inbred chick with a highly inbred parent inherits a "proven" genotype and thus experiences a fitness advantage, which could explain the interaction. The positive and negative effects we found emphasize that continuing inbreeding can have important effects on individual fitness, even in populations that are already highly inbred.

Exploring a Tomato Landraces Collection for Fruit-Related Traits by the Aid of a High-Throughput Genomic Platform.

During its evolution and domestication Solanum lycopersicum has undergone various genetic ‘bottlenecks’ and extreme inbreeding of limited genotypes. In Europe the tomato found a secondary centre for diversification, which resulted in a wide array of fruit shape variation given rise to a range of landraces that have been cultivated for centuries. Landraces represent a reservoir of genetic diversity especially for traits such as abiotic stress resistance and high fruit quality. Information about the variation present among tomato landrace populations is still limited. A collection of 123 genotypes from different geographical areas was established with the aim of capturing a wide diversity. Eighteen morphological traits were evaluated, mainly related to the fruit. About 45% of morphological variation was attributed to fruit shape, as estimated by the principal component analysis, and the dendrogram of relatedness divided the population in subgroups mainly on the basis of fruit weight and locule number. Genotyping was carried out using the tomato array platform SolCAP able to interrogate 7,720 SNPs. In the whole collection 87.1% markers were polymorphic but they decreased to 44–54% when considering groups of genotypes with different origin. The neighbour-joining tree analysis clustered the 123 genotypes into two main branches. The STRUCTURE analysis with K = 3 also divided the population on the basis of fruit size. A genomic-wide association strategy revealed 36 novel markers associated to the variation of 15 traits. The markers were mapped on the tomato chromosomes together with 98 candidate genes for the traits analyzed. Six regions were evidenced in which candidate genes co-localized with 19 associated SNPs. In addition, 17 associated SNPs were localized in genomic regions lacking candidate genes. The identification of these markers demonstrated that novel variability was captured in our germoplasm collection. They might also provide a viable indirect selection tool in future practical breeding programs.

Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis.

The nematode Caenorhabditis briggsae is a model for comparative developmental evolution with C. elegans. Worldwide collections of C. briggsae have implicated an intriguing history of divergence among genetic groups separated by latitude, or by restricted geography, that is being exploited to dissect the genetic basis to adaptive evolution and reproductive incompatibility; yet, the genomic scope and timing of population divergence is unclear. We performed high-coverage whole-genome sequencing of 37 wild isolates of the nematode C. briggsae and applied a pairwise sequentially Markovian coalescent (PSMC) model to 703 combinations of genomic haplotypes to draw inferences about population history, the genomic scope of natural selection, and to compare with 40 wild isolates of C. elegans. We estimate that a diaspora of at least six distinct C. briggsae lineages separated from one another approximately 200,000 generations ago, including the “Temperate” and “Tropical” phylogeographic groups that dominate most samples worldwide. Moreover, an ancient population split in its history approximately 2 million generations ago, coupled with only rare gene flow among lineage groups, validates this system as a model for incipient speciation. Low versus high recombination regions of the genome give distinct signatures of population size change through time, indicative of widespread effects of selection on highly linked portions of the genome owing to extreme inbreeding by self-fertilization. Analysis of functional mutations indicates that genomic context, owing to selection that acts on long linkage blocks, is a more important driver of population variation than are the functional attributes of the individually encoded genes.

Outbreeding effects in an inbreeding insect, Cimex lectularius

In some species, populations with few founding individuals can be resilient to extreme inbreeding. Inbreeding seems to be the norm in the common bed bug, Cimex lectularius, a flightless insect that, nevertheless, can reach large deme sizes and persist successfully. However, bed bugs can also be dispersed passively by humans, exposing inbred populations to gene flow from genetically distant populations. The introduction of genetic variation through this outbreeding could lead to increased fitness (heterosis) or be costly by causing a loss of local adaptation or exposing genetic incompatibility between populations (outbreeding depression). Here, we addressed how inbreeding within demes and outbreeding between distant populations impact fitness over two generations in this re-emerging public health pest. We compared fitness traits of families that were inbred (mimicking reproduction following a founder event) or outbred (mimicking reproduction following a gene flow event). We found that outbreeding led to increased starvation resistance compared to inbred families, but this benefit was lost after two generations of outbreeding. No other fitness benefits of outbreeding were observed in either generation, including no differences in fecundity between the two treatments. Resilience to inbreeding is likely to result from the history of small founder events in the bed bug. Outbreeding benefits may only be detectable under stress and when heterozygosity is maximized without disruption of coadaptation. We discuss the consequences of these results both in terms of inbreeding and outbreeding in populations with genetic and spatial structuring, as well as for the recent resurgence of bed bug populations.

Influence of Inbreeding on Female Mate Choice in Two Species of Drosophila.

Many organisms have been reported to choose their mates in order to increase the heterozygosity of their offspring by avoiding mating with relatives or homozygous individuals. Most previous studies using Drosophila melanogaster have used artificial chromosomes or extreme inbreeding treatments, situations unlikely to be matched in nature. Additionally, few studies have examined the interaction between female inbreeding status and her choice of mate. Using females and males from populations that had experienced either random mating or one generation of sib-sib inbreeding, we measured the preferences of females for males. Our results indicate that outbred males were chosen more often than inbred males and that this preference may be more pronounced in outbred females than in inbred ones.