A comparison of pedigree‐ and DNA‐based measures for identifying inbreeding depression in the critically endangered Attwater's Prairie‐chicken

The primary goal of captive breeding programmes for endangered species is to prevent extinction, a component of which includes the preservation of genetic diversity and avoidance of inbreeding. This is typically accomplished by minimizing mean kinship in the population, thereby maintaining equal representation of the genetic founders used to initiate the captive population. If errors in the pedigree do exist, such an approach becomes less effective for minimizing inbreeding depression. In this study, both pedigree‐ and DNA‐based methods were used to assess whether inbreeding depression existed in the captive population of the critically endangered Attwater's Prairie‐chicken (Tympanuchus cupido attwateri), a subspecies of prairie grouse that has experienced a significant decline in abundance and concurrent reduction in neutral genetic diversity. When examining the captive population for signs of inbreeding, variation in pedigree‐based inbreeding coefficients (f_pedigree) was less than that obtained from DNA‐based methods (f_DNA). Mortality of chicks and adults in captivity were also positively correlated with parental relatedness (r_DNA) and f_DNA, respectively, while no correlation was observed with pedigree‐based measures when controlling for additional variables such as age, breeding facility, gender and captive/release status. Further, individual homozygosity by loci (HL) and parental r_DNA values were positively correlated with adult mortality in captivity and the occurrence of a lethal congenital defect in chicks, respectively, suggesting that inbreeding may be a contributing factor increasing the frequency of this condition among Attwater's Prairie‐chickens. This study highlights the importance of using DNA‐based methods to better inform management decisions when pedigrees are incomplete or errors may exist due to uncertainty in pairings.     

Genome-wide population structure and evolutionary history of the Frizarta dairy sheep

In the present study, we used genomic data, generated with a medium density single nucleotide polymorphisms (SNP) array, to acquire more information on the population structure and evolutionary history of the synthetic Frizarta dairy sheep. First, two typical measures of linkage disequilibrium (LD) were estimated at various physical distances that were then used to make inferences on the effective population size at key past time points. Population structure was also assessed by both multidimensional scaling analysis and k-means clustering on the distance matrix obtained from the animals’ genomic relationships. The Wright’s fixation F_ST index was also employed to assess herds’ genetic homogeneity and to indirectly estimate past migration rates. The Wright’s fixation F_IS index and genomic inbreeding coefficients based on the genomic relationship matrix as well as on runs of homozygosity were also estimated. The Frizarta breed displays relatively low LD levels with r² and |Dʹ| equal to 0.18 and 0.50, respectively, at an average inter-marker distance of 31 kb. Linkage disequilibrium decayed rapidly by distance and persisted over just a few thousand base pairs. Rate of LD decay (β) varied widely among the 26 autosomes with larger values estimated for shorter chromosomes (e.g. β=0.057, for OAR6) and smaller values for longer ones (e.g. β=0.022, for OAR2). The inferred effective population size at the beginning of the breed’s formation was as high as 549, was then reduced to 463 in 1981 (end of the breed’s formation) and further declined to 187, one generation ago. Multidimensional scaling analysis and k-means clustering suggested a genetically homogenous population, F_ST estimates indicated relatively low genetic differentiation between herds, whereas a heat map of the animals’ genomic kinship relationships revealed a stratified population, at a herd level. Estimates of genomic inbreeding coefficients suggested that most recent parental relatedness may have been a major determinant of the current effective population size. A denser than the 50k SNP panel may be more beneficial when performing genome wide association studies in the breed.     

An evaluation of inbreeding measures using a whole-genome sequenced cattle pedigree

The estimation of the inbreeding coefficient (F) is essential for the study of inbreeding depression (ID) or for the management of populations under conservation. Several methods have been proposed to estimate the realized F using genetic markers, but it remains unclear which one should be used. Here we used whole-genome sequence data for 245 individuals from a Holstein cattle pedigree to empirically evaluate which estimators best capture homozygosity at variants causing ID, such as rare deleterious alleles or loci presenting heterozygote advantage and segregating at intermediate frequency. Estimators relying on the correlation between uniting gametes (F_UNI) or on the genomic relationships (F_GRM) presented the highest correlations with these variants. However, homozygosity at rare alleles remained poorly captured. A second group of estimators relying on excess homozygosity (F_HOM), homozygous-by-descent segments (F_HBD), runs-of-homozygosity (F_ROH) or on the known genealogy (F_PED) was better at capturing whole-genome homozygosity, reflecting the consequences of inbreeding on all variants, and for young alleles with low to moderate frequencies (0.10 < . < 0.25). The results indicate that F_UNI and F_GRM might present a stronger association with ID. However, the situation might be different when recessive deleterious alleles reach higher frequencies, such as in populations with a small effective population size. For locus-specific inbreeding measures or at low marker density, the ranking of the methods can also change as F_HBD makes better use of the information from neighboring markers. Finally, we confirmed that genomic measures are in general superior to pedigree-based estimates. In particular, F_PED was uncorrelated with locus-specific homozygosity.Subject terms: Conservation genomics, Animal breeding, Inbreeding     

Pedigree analysis of the Turkish Arab horse population: structure,inbreeding and genetic variability

The aim of this study was to evaluate genetic variability in the Turkish Arab horse population using pedigree information. This study is the first detailed pedigree analysis of the breed in Turkey. Pedigree data were collected from the National Studbook. The pedigree data for 23 668 horses, born between 1904 and 2014, were used in the analysis. From this data set, a reference population (RP) of 14 838 animals symbolising the last generation was defined. Demographic parameters, the inbreeding level (F), the average relatedness (AR), the effective population size (N_e), the effective number of founders (f_e), the effective number of ancestors (f_a) and the number of founder genome equivalents (f_g) were calculated for the population. The average generation interval for the RP was 12.2±4.6 years, whereas the calculated pedigree completeness levels were 98.2%, 96.6% and 95.0% for the first, second and third known generations. The mean equivalent generations (t), the average complete generations and the mean maximum generations for the RP were 7.8, 5.4 and 12.2, respectively, whereas the meanFand AR were 4.6% and 9.5% for the RP. The rate of inbred animals was 94.2% for the RP, whereas the number of founders, the number of ancestors and thef_e,f_aandf_gwere 342, 223, 40, 22 and 9.6 for the RP. The large differences observed betweenf_e, and the number of founders demonstrates that genetic diversity decreased between the founder and the RP. Contribution of the 14 most influential founder to the RP was 50.0%, whereas just eight ancestral horses can account for 50% of the genetic variability.N_eestimated via an individual increase in inbreeding per generation (${\overline{N}}_{\text{e}}$), and paired increase in coancestry$\left(\text{}{\overline{N}}_{eC}\right)$, were 74.4±3.9 and 73.5±0.58, respectively. The inbreeding increases with the pedigree knowledge. In addition, the decrease in inbreeding in last years is more noticeable.     

Sustainability of the South China tiger: implications of inbreeding depression and introgression

The South China tiger (Panther tigris amoyensis) is critically endangered with 73 remaining individuals living in captivity, all derived from six wild founders since 1963. The population shows a low level of juvenile survivorship and reproductive difficulties, and faces a huge conservation challenge. In this study, inbreeding depression and genetic diversity decline were examined by using pedigree data and 17 microsatellites. The constant B, which is related to the number of lethal equivalents, was estimated to be 0 for the offspring of noninbred parents, but was >0 for the offspring of inbred parents and for all offspring. Percentage of successfully breeding tigers inversely correlated with inbreeding level (r = −0.626, α = 0.05). Taken together, these findings suggest the population is suffering from inbreeding depression in juvenile survivorship and fecundity. No significant correlation was detectable for the mean litter size with f of either dams (r = −0.305, α = 0.46) or kittens (r = 0.105, α = 0.71), indicating litter size was not strongly subject to inbreeding depression. The average number of alleles per locus was 4.24 ± 1.03 (SE), but effective number of alleles was only 2.53 ± 0.91. Twenty-one alleles carried by early breeders at 13 loci were absent in the present breeders and potential breeders. Multilocus heterozygosity was inversely correlated with inbreeding levels (r = −0.601, α = 0.004). These findings suggest rapid allelic diversity loss is occurring in this small captive population and that heterozygosity is being lost as it becomes more inbred. Our phylogenetic analysis supports past work indicating introgression from northern Indochinese tigers in the population. As no wild representatives of the South China tiger can be added to the captive population, we may consider the alternate scenario of further introgression in the interest of countering inbreeding depression and declining genetic diversity.     

Effective Population Size,Extended Linkage Disequilibrium and Signatures of Selection in the Rare Dog Breed Lundehund

The Lundehund is an old dog breed with remarkable anatomical features including polydactyly in all four limbs and extraordinary flexibility of the spine. We genotyped 28 Lundehund using the canine Illumina high density beadchip to estimate the effective population size (N_e) and inbreeding coefficients as well as to identify potential regions of positive selection. The decay of linkage disequilibrium was slow with r² = 0.95 in 50 kb distance. The last 7-200 generations ago, Ne was at 10-13. An increase of N_e was noted in the very recent generations with a peak value of 19 for N_e at generation 4. The FROH estimated for 50-, 65- and 358-SNP windows were 0.87, 087 and 0.81, respectively. The most likely estimates for F_ROH after removing identical-by-state segments due to linkage disequilibria were at 0.80-0.81. The extreme loss of heterozygosity has been accumulated through continued inbreeding over 200 generations within a probably closed population with a small effective population size. The mean inbreeding coefficient based on pedigree data for the last 11 generations (F_Ped = 0.10) was strongly biased downwards due to the unknown coancestry of the founders in this pedigree data. The long-range haplotype test identified regions with genes involved in processes of immunity, olfaction, woundhealing and neuronal development as potential targets of selection. The genes QSOX2, BMPR1B and PRRX2 as well as MYOM1 are candidates for selection on the Lundehund characteristics small body size, increased number of digits per paw and extraordinary mobility, respectively.     

Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds

In the local breeds with small population size, one of the most important problems is the increase of inbreeding coefficient (F). High levels of inbreeding lead to reduced genetic diversity and inbreeding depression. The availability of high-density single nucleotide polymorphism (SNP) arrays has facilitated the quantification of F by genomic markers in farm animals. Runs of homozygosity (ROH) are contiguous lengths of homozygous genotypes and represent an estimate of the degree of autozygosity at genome-wide level. The current study aims to quantify the genomic F derived from ROH (F_ROH) in three local dairy cattle breeds. F_ROH values were compared with F estimated from the genomic relationship matrix (F_GRM), based on the difference between observed v. expected number of homozygous genotypes (F_HOM) and the genomic homozygosity of individual i (F_{MOL i}). The molecular coancestry coefficient (f_{MOL ij}) between individuals i and j was also estimated. Individuals of Cinisara (71), Modicana (72) and Reggiana (168) were genotyped with the 50K v2 Illumina BeadChip. Genotypes from 96 animals of Italian Holstein cattle breed were also included in the analysis. We used a definition of ROH as tracts of homozygous genotypes that were >4 Mb. Among breeds, 3661 ROH were identified. Modicana showed the highest mean number of ROH per individual and the highest value of F_ROH, whereas Reggiana showed the lowest ones. Differences among breeds existed for the ROH lengths. The individuals of Italian Holstein showed high number of short ROH segments, related to ancient consanguinity. Similar results showed the Reggiana with some extreme animals with segments covering 400 Mb and more of genome. Modicana and Cinisara showed similar results between them with the total length of ROH characterized by the presence of large segments. High correlation was found between F_HOM and F_ROH ranged from 0.83 in Reggiana to 0.95 in Cinisara and Modicana. The correlations among F_ROH and other estimated F coefficients were generally lower ranged from 0.45 (F_{MOL i}−F_ROH) in Cinisara to 0.17 (F_GRM−F_ROH) in Modicana. On the basis of our results, recent inbreeding was observed in local breeds, considering that 16 Mb segments are expected to present inbreeding up to three generations ago. Our results showed the necessity of implementing conservation programs to control the rise of inbreeding and coancestry in the three Italian local dairy cattle breeds.     

Genome-wide single nucleotide polymorphisms (SNPs) for a model invasive ascidian <Emphasis Type="Italic">Botryllus schlosseri</Emphasis>

Invasive species cause huge damages to ecology, environment and economy globally. The comprehensive understanding of invasion mechanisms, particularly genetic bases of micro-evolutionary processes responsible for invasion success, is essential for reducing potential damages caused by invasive species. The golden star tunicate, Botryllus schlosseri, has become a model species in invasion biology, mainly owing to its high invasiveness nature and small well-sequenced genome. However, the genome-wide genetic markers have not been well developed in this highly invasive species, thus limiting the comprehensive understanding of genetic mechanisms of invasion success. Using restriction site-associated DNA (RAD) tag sequencing, here we developed a high-quality resource of 14,119 out of 158,821 SNPs for B. schlosseri. These SNPs were relatively evenly distributed at each chromosome. SNP annotations showed that the majority of SNPs (63.20%) were located at intergenic regions, and 21.51% and 14.58% were located at introns and exons, respectively. In addition, the potential use of the developed SNPs for population genomics studies was primarily assessed, such as the estimate of observed heterozygosity (H _O ), expected heterozygosity (H _E ), nucleotide diversity (π), Wright’s inbreeding coefficient (F _IS ) and effective population size (Ne). Our developed SNP resource would provide future studies the genome-wide genetic markers for genetic and genomic investigations, such as genetic bases of micro-evolutionary processes responsible for invasion success.     

EFFECTIVE POPULATION SIZE IN A CONTINUOUSLY DISTRIBUTED POPULATION

An individual-based simulation model was created to examine genetic variability, time until fixation and spatial genetic structure in a continuously distributed population. Previous mathematical models for continuously distributed populations have the difficulty that the assumption of independent reproduction and independent dispersal of offspring cause clumped spatial distribution and thus violate an assumption of random spatial distribution. In this study, this problem is avoided by considering the dispersal behavior of offspring. The simulation results showed that the inbreeding effective population size estimated by the rate of decrease of heterozygosity during the first 15 generations corresponds to the neighborhood size calculated by the standard deviation of the dispersal distance (σ_T). This inbreeding effective population size does not greatly change with the area of simulation when the densities and σ_T are the same. However, the inbreeding effective population size estimated by heterozygosity using the first 500 generations is larger than the neighborhood size calculated by the dispersal distance and increases with the area of simulation with the same densities. The variance effective population size, estimated by time until fixation of alleles, increases with dispersal distance (σ_T) and with the area of simulation given the same densities. The inbreeding effective population size and variance effective population size were smaller than the actual population size unless σ_T is sufficiently large (2 σ_T > approximate L/2, where L is a side of the simulation square).     

Comparative evaluation of genomic inbreeding parameters in seven commercial and autochthonous pig breeds

Single nucleotide polymorphism (SNP) genotyping tools, which can analyse thousands of SNPs covering the whole genome, have opened new opportunities to estimate the inbreeding level of animals directly using genome information. One of the most commonly used genomic inbreeding measures considers the proportion of the autosomal genome covered by runs of homozygosity (ROH), which are defined as continuous and uninterrupted chromosome portions showing homozygosity at all loci. In this study, we analysed the distribution of ROH in three commercial pig breeds (Italian Large White, n = 1968; Italian Duroc, n = 573; and Italian Landrace, n = 46) and four autochthonous breeds (Apulo-Calabrese, n = 90; Casertana, n = 90; Cinta Senese, n = 38; and Nero Siciliano, n = 48) raised in Italy, using SNP data generated from Illumina PorcineSNP60 BeadChip. We calculated ROH-based inbreeding coefficients (F_ROH) using ROH of different minimum length (1, 2, 4, 8, 16 Mbp) and compared them with several other genomic inbreeding coefficients (including the difference between observed and expected number of homozygous genotypes (F_HOM)) and correlated all these genomic-based measures with the pedigree inbreeding coefficient (F_PED) calculated for the pigs of some of these breeds. Autochthonous breeds had larger mean size of ROH than all three commercial breeds. F_HOM was highly correlated (0.671 to 0.985) with F_ROH measures in all breeds. Apulo-Calabrese and Casertana had the highest F_ROH values considering all ROH minimum lengths (ranging from 0.273 to 0.189 and from 0.226 to 0.152, moving from ROH of minimum size of 1 Mbp (F_ROH1) to 16 Mbp (F_ROH16)), whereas the lowest F_ROH values were for Nero Siciliano (from 0.072 to 0.051) and Italian Large White (from 0.117 to 0.042). F_ROH decreased as the minimum length of ROH increased for all breeds. Italian Duroc had the highest correlations between all F_ROH measures and F_PED (from 0.514 to 0.523) and between F_HOM and F_PED (0.485). Among all analysed breeds, Cinta Senese had the lowest correlation between F_ROH and F_PED. This might be due to the imperfect measure of F_PED, which, mainly in local breeds raised in extensive production systems, cannot consider a higher level of pedigree errors and a potential higher relatedness of the founder population. It appeared that ROH better captured inbreeding information in the analysed breeds and could complement pedigree-based inbreeding coefficients for the management of these genetic resources.     

Analysis of founders and performance test effects on an autochthonous horse population through pedigree analysis: structure,genetic variability and inbreeding

The Maremmano is an autochthonous Italian horse breed, which probably descended from the native horses of the Etruscans (VI century B.C.); the Studbook was acknowledged in 1980, and it includes 12 368 horses born from that year up to 2015. The aim of this study was to evaluate the effect of the selection program on the genetic variability of the Maremmano population; the analysis was performed using both the ‘Endog v 4.8’ program available at http://webs.ucm.es/info/prodanim/html/JP_Web.htm and in-house software on official pedigree data. Four Reference Populations were considered, and the most important one was the population of the 12 368 Maremmano horses officially registered in the National Studbook. The pedigree completeness of this population was very good because it was more than 90% at the third parental generation and more than 70% at the fifth generation; the pedigree traced back to a maximum of 10.50 generations with an average of 3.30 complete generations and 5.70 equivalent complete generations. The average generation interval was 10.65±4.72 years, with stallions used for longer periods than mares. The intervals ranged from 10.15±4.45 (mother–daughter) to 10.99±4.93 (father–daughter). The effective number of founders (f_e) was 74 and the effective number of ancestors (f_a) was 30 so that the ratio f_e/f_a was 2.47. The founder genome equivalents (f_g) was 13.72 with a ratio f_g/f_e equal to 0.18. The mean of the genetic conservation index was 5.55±3.37, and it ranged from 0.81 to 21.32. The average inbreeding coefficient was 2.94%, with an increase of 0.1%/year, and the average relatedness coefficient was 5.52%. The effective population size (N_e) computed by an individual increase in inbreeding was 68.1±13.00; the N_e on equivalent generations was 42.00, and this value slightly increased to 42.20 when computed by Log regression on equivalent generations. The analysis confirmed the presence of seven traditional male lines. The percentage of Thoroughbred blood in the foals born in 2015 was 20.30% and has increased 0.21%/year since 1980; in particular, it increased more than twice (0.51%/year) until 1993 and afterwards slightly fluctuated. The pedigree analysis confirmed the completeness of genealogical information and the traditional importance that breeders gave to the male lines; although the genetic diversity of Maremmano seemed to be not endangered by the selection program, some effects on the population structure were found and a more scientific approach to genetic conservation should be incorporated in the selection plans.     

Genetic diversity and structure of an endemic and critically endangered stream river salamander (Caudata: Ambystoma leorae) in Mexico

Small or isolated populations are highly susceptible to stochastic events. They are prone and vulnerable to random demographic or environmental fluctuations that could lead to extinction due to the loss of alleles through genetic drift and increased inbreeding. We studied Ambystoma leorae an endemic and critically threatened species. We analyzed the genetic diversity and structure, effective population size, presence of bottlenecks and inbreeding coefficient of 96 individuals based on nine microsatellite loci. We found high levels of genetic diversity expressed as heterozygosity (H_o = 0.804, H_e = 0.613, H_e* = 0.626 and H_Nei = 0.622). The population presents few alleles (4–9 per locus) and genotypes (3–14 per locus) compared with other mole salamanders species. We identified three genetically differentiated subpopulations with a significant level of genetic structure (F_ST = 0.021, R_ST = 0.044 y D_est = 0.010, 95 % CI). We also detected a reduction signal in population size and evidence of a genetic bottleneck (M = 0.367). The effective population size is small (Ne = 45.2), but similar to another mole salamanders with restricted distributions or with recently fragmented habitat. The inbreeding coefficient levels detected are low (F_IS = ?0.619–0.102) as is gene flow. Despite, high levels of genetic diversity A. leorae is critically endangered because it is a small isolated population.     

Increased inbreeding but not homozygosity in small populations of Sabatia angularis (Gentianaceae)

Understanding how the mating system varies with population size in plant populations is critical for understanding their genetic and demographic fates. We examined how the mating system, characterized by outcrossing rate, biparental inbreeding rate, and inbreeding coefficient, and genetic diversity varied with population size in natural populations of the biennial Sabatia angularis. We found a significant, positive relationship between outcrossing and population size. Selfing was as high as 40% in one small population but was only 7% in the largest population. Despite this pattern, observed heterozygosity did not vary with population size, and we suggest that selection against inbred individuals maintains observed heterozygosity in small populations. Consistent with this hypothesis, we found a trend of lower inbreeding coefficients in the maternal than progeny generation in all of the populations, and half of the populations exhibited significant excesses of adult heterozygosity. Moreover, genetic diversity was not related to population size and was similar across all populations examined. Our results suggest that the consequences of increased selfing for population fitness in S. angularis, a species that experiences significant inbreeding depression, will depend on the relative magnitude and consistency of inbreeding depression and the demographic cost of selection for outcrossed progeny in small populations.     

Inference of population structure of purebred dairy and beef cattle using high-density genotype data

Information on the genetic diversity and population structure of cattle breeds is useful when deciding the most optimal, for example, crossbreeding strategies to improve phenotypic performance by exploiting heterosis. The present study investigated the genetic diversity and population structure of the most prominent dairy and beef breeds used in Ireland. Illumina high-density genotypes (777 962 single nucleotide polymorphisms; SNPs) were available on 4623 purebred bulls from nine breeds; Angus (n=430), Belgian Blue (n=298), Charolais (n=893), Hereford (n=327), Holstein-Friesian (n=1261), Jersey (n=75), Limousin (n=943), Montbéliarde (n=33) and Simmental (n=363). Principal component analysis revealed that Angus, Hereford, and Jersey formed non-overlapping clusters, representing distinct populations. In contrast, overlapping clusters suggested geographical proximity of origin and genetic similarity between Limousin, Simmental and Montbéliarde and to a lesser extent between Holstein, Friesian and Belgian Blue. The observed SNP heterozygosity averaged across all loci was 0.379. The Belgian Blue had the greatest mean observed heterozygosity (H_O=0.389) among individuals within breed while the Holstein-Friesian and Jersey populations had the lowest mean heterozygosity (H_O=0.370 and 0.376, respectively). The correlation between the genomic-based and pedigree-based inbreeding coefficients was weak (r=0.171; P<0.001). Mean genomic inbreeding estimates were greatest for Jersey (0.173) and least for Hereford (0.051). The pair-wise breed fixation index (F_st) ranged from 0.049 (Limousin and Charolais) to 0.165 (Hereford and Jersey). In conclusion, substantial genetic variation exists among breeds commercially used in Ireland. Thus custom-mating strategies would be successful in maximising the exploitation of heterosis in crossbreeding strategies.     

Quantifying realized inbreeding in wild and captive animal populations

Most molecular measures of inbreeding do not measure inbreeding at the scale that is most relevant for understanding inbreeding depression—namely the proportion of the genome that is identical-by-descent (IBD). The inbreeding coefficient F_Ped obtained from pedigrees is a valuable estimator of IBD, but pedigrees are not always available, and cannot capture inbreeding loops that reach back in time further than the pedigree. We here propose a molecular approach to quantify the realized proportion of the genome that is IBD (propIBD), and we apply this method to a wild and a captive population of zebra finches (Taeniopygia guttata). In each of 948 wild and 1057 captive individuals we analyzed available single-nucleotide polymorphism (SNP) data (260 SNPs) spread over four different genomic regions in each population. This allowed us to determine whether any of these four regions was completely homozygous within an individual, which indicates IBD with high confidence. In the highly nomadic wild population, we did not find a single case of IBD, implying that inbreeding must be extremely rare (propIBD=0–0.00094, 95% CI). In the captive population, a five-generation pedigree strongly underestimated the average amount of realized inbreeding (F_Ped=0.013<propIBD=0.064), as expected given that pedigree founders were already related. We suggest that this SNP-based technique is generally useful for quantifying inbreeding at the individual or population level, and we show analytically that it can capture inbreeding loops that reach back up to a few hundred generations.     

Measures of Autozygosity in Decline: Globalization, Urbanization, and Its Implications for Medical Genetics

This research investigates the influence of demographic factors on human genetic sub-structure. In our discovery cohort, we show significant demographic trends for decreasing autozygosity associated with population variation in chronological age. Autozygosity, the genomic signature of consanguinity, is identifiable on a genome-wide level as extended tracts of homozygosity. We identified an average of 28.6 tracts of extended homozygosity greater than 1 Mb in length in a representative population of 809 unrelated North Americans of European descent ranging in chronological age from 19–99 years old. These homozygous tracts made up a population average of 42 Mb of the genome corresponding to 1.6% of the entire genome, with each homozygous tract an average of 1.5 Mb in length. Runs of homozygosity are steadily decreasing in size and frequency as time progresses (linear regression, p<0.05). We also calculated inbreeding coefficients and showed a significant trend for population-wide increasing heterozygosity outside of linkage disequilibrium. We successfully replicated these associations in a demographically similar cohort comprised of a subgroup of 477 Baltimore Longitudinal Study of Aging participants. We also constructed statistical models showing predicted declining rates of autozygosity spanning the 20th century. These predictive models suggest a 14.0% decrease in the frequency of these runs of homozygosity and a 24.3% decrease in the percent of the genome in runs of homozygosity, as well as a 30.5% decrease in excess homozygosity based on the linkage pruned inbreeding coefficients. The trend for decreasing autozygosity due to panmixia and larger effective population sizes will likely affect the frequency of rare recessive genetic diseases in the future. Autozygosity has declined, and it seems it will continue doing so.     

Association between host's genetic diversity and parasite burden in damselflies

Recent research indicates that low genetic variation in individuals can increase susceptibility to parasite infection, yet evidence from natural invertebrate populations remains scarce. Here, we studied the relationship between genetic heterozygosity, measured as AFLP‐based inbreeding coefficient f_AFLP, and gregarine parasite burden from eleven damselfly, Calopteryx splendens, populations. We found that in the studied populations, 5–92% of males were parasitized by endoparasitic gregarines (Apicomplexa: Actinocephalidae). Number of parasites ranged from none to 47 parasites per male, and parasites were highly aggregated in a few hosts. Mean individual f_AFLP did not differ between populations. Moreover, we found a positive association between individual's inbreeding coefficient and parasite burden. In other words, the more homozygous the individual, the more parasites it harbours. Thus, parasites are likely to pose strong selection pressure against inbreeding and homozygosity. Our results support the heterozygosity‐fitness correlation hypothesis, which suggests the importance of heterozygosity for an individual's pathogen resistance.     

Development of robust genomic simple sequence repeat markers for estimation of genetic diversity within and among bulb onion (Allium cepa L.) populations

Improved understanding of genetic diversity in onion and shallot (Allium cepa L.) is required to inform breeding and genetic resource conservation, and to enable development of association genetics and seed quality assurance methods. To develop quantitative estimates of diversity we estimated within- and among-population heterozygosity in a set of onion populations using genomic simple sequence repeat (SSR) markers developed by genomic skim sequencing. Primer sets (166) designed to flank SSR motifs identified were evaluated in a diverse set of lines, with 80 (48?%) being polymorphic. The 20 most robust single copy markers were scored in 12 individuals from 24 populations representing short-day to long-day adapted material from diverse environments. The average genetic diversity estimate (H _e) per population was 0.3 (SD 0.08) and the average per marker was 0.49 (SD 0.2). The onion populations assessed in this survey were distinct with moderate to large population differentiation but also had high within-population variation (F _st?=?0.26). There was evidence of inbreeding (F _is?=?0.22) with observed heterozygosities lower than the expected. This marker resource will be applicable for DNA fingerprinting, measuring levels of inbreeding in breeding lines, assessing population structure for association mapping and expanding linkage maps that are principally based on expressed sequence tag-based markers. A Galaxy workflow was developed to facilitate bulk SSR marker design from next-generation sequence data. This study provides one of the first quantitative views of population genetic variation in onion and a practical toolset for further genetics.     

Regions of Homozygosity in the Porcine Genome: Consequence of Demography and the Recombination Landscape

Inbreeding has long been recognized as a primary cause of fitness reduction in both wild and domesticated populations. Consanguineous matings cause inheritance of haplotypes that are identical by descent (IBD) and result in homozygous stretches along the genome of the offspring. Size and position of regions of homozygosity (ROHs) are expected to correlate with genomic features such as GC content and recombination rate, but also direction of selection. Thus, ROHs should be non-randomly distributed across the genome. Therefore, demographic history may not fully predict the effects of inbreeding. The porcine genome has a relatively heterogeneous distribution of recombination rate, making Sus scrofa an excellent model to study the influence of both recombination landscape and demography on genomic variation. This study utilizes next-generation sequencing data for the analysis of genomic ROH patterns, using a comparative sliding window approach. We present an in-depth study of genomic variation based on three different parameters: nucleotide diversity outside ROHs, the number of ROHs in the genome, and the average ROH size. We identified an abundance of ROHs in all genomes of multiple pigs from commercial breeds and wild populations from Eurasia. Size and number of ROHs are in agreement with known demography of the populations, with population bottlenecks highly increasing ROH occurrence. Nucleotide diversity outside ROHs is high in populations derived from a large ancient population, regardless of current population size. In addition, we show an unequal genomic ROH distribution, with strong correlations of ROH size and abundance with recombination rate and GC content. Global gene content does not correlate with ROH frequency, but some ROH hotspots do contain positive selected genes in commercial lines and wild populations. This study highlights the importance of the influence of demography and recombination on homozygosity in the genome to understand the effects of inbreeding.     

Runs of homozygosity have utility in mammalian conservation and evolutionary studies

Runs of homozygosity (ROHs) arise due the transmission from parents to offspring of segments that are either identical by decent (IBD) or identical by state (IBS). The former is due to consanguineous matings whereas the latter is due to demographic processes. ROHs reduce individual nucleotide diversity (θ) as a function of homozygosity, and thus ROH distributions and θ are expected to vary among species because inbreeding levels, recombination rates, and demographic histories vary widely. To help interpret genetic diversity within and among species, we utilized genome sequence data from 78 mammalian species to compare θ and ROH burden (i.e., number and length of ROHs in the genome) among groups of mammals to assess genomic signatures of inbreeding. We compared θ and ROHs: (i) among threatened and non-threatened mammals to determine the significance of contemporary conservation status; (ii) among carnivorous and non-carnivorous mammals to determine the relevance of trophic effects; (iii) relative to body size because mutation rates generally vary with body mass; and (iv) across mammals from different latitudes to test for gradients in genomic diversity (e.g., due to effects of historic climatic regimes). Our results illustrate the considerable variance in genomic diversity across mammals, and that trophic level, body mass, and latitude have significant effects on θ and ROH burden. However, conservation status was not a reliable indicator of genomic diversity. We argue that genetic or genomic diversity should be an explicit component of conservation status, as such diversity is critical to the long-term sustainability of populations, and anticipate that ROHs will become more commonly used to estimate inbreeding in wild animals.