Genetic Connectedness Research Articles

The Epic of Evolution and a Theology of Sacramental Ecology

The ‘Epic of Evolution’ is the scientific story that reveals that we live in an approximately 14-billion-year-old universe on a planet that is approximately 4.6 billion years old and that we are a part of the ongoing process of life that has existed on Earth for 3.5–4 billion years. This article focuses on the religious and ecological significance of the evolutionary epic in an effort to seamlessly connect the ecological value attributed as a part of an understanding of the evolutionary connectedness of life on earth with the Divine grace understood to be present in Christian sacramental worship. With a particular emphasis on the Eucharist, I argue that the sacramental perspective of grace being conveyed through material reality provides the potential for Christian sacramental tradition to make a significant contribution to protecting the threatened ecological communities of our planet. By incorporating William Temple’s concept of a ‘sacramental universe,’ I propose that the grace that is understood to be present in the substances of the bread and wine of the Eucharist points outward so that it can also be witnessed in all of God’s ongoing Creation. When the Eucharist is understood as taking place in a sacramental universe from which ecological grace flows; the incarnation can be recognized not as a one-time event but as an ongoing sacramental process through which God is revealed through the perpetual emergence of life. Consequently, as the primary form of sacramental worship in Christian tradition, the Eucharistic witness to the incarnation of God in Jesus and thanksgiving for life overcoming death provide Christians with a ritual orientation for recognizing the incarnational presence of God as an ever-present reality potentially witnessed in all that is. Therefore, the formal sacrament of the Eucharist is a part of a broader sacramental ecology of earthly life in which the presence of Divine grace can be witnessed in all aspects of the natural order. As a result, connecting Eucharistic grace with the value associated with an awareness of the ecological and genetic connectedness of all forms of life serves as a mutual enrichment of sacramental tradition and contemporary efforts to protect life on Earth.

Un/familiar connections: on the relevance of a sociology of personal life for exploring egg and sperm donation.

In recent decades, reproductive medicine has become a widespread global phenomenon. Within the field, donor conception, and the use of donated eggs, sperm or embryos from a third party, plays a key role. Despite the importance of those individuals who donate, there has been scant research exploring their experiences. Seeking to contribute to the growing, albeit still small, body of research on donors, this paper advocates bringing the process of donating into dialogue with a sociology of personal life. It suggests that important new insights about the donor experience can be achieved by utilising such a theoretical perspective. The paper applies a broad framework of a sociology of personal life to demonstrate that the decision to donate reverberates within donors’ everyday lives and relationships, and explores, primarily theoretically, how it is that acts of donation bring such issues into play. To this end, the paper examines in detail three ways in which donating interacts with dimensions that are integral to personal life: “living” genetic connectedness, relationality and the intimate body. Ultimately, the paper suggests that a sociology of personal life shows light on new, unexplored questions for this field that demand greater scholarly attention.

Genetic improvement of resistance to cyclaneusma needle cast in Pinus radiata

Progeny testing of resistance to needle loss caused by Cyclaneusma minus (cyclaneusma needle cast) has been included in the needle disease resistance strategy of Pinus radiata D. Don in New Zealand since the late 1970s. Data on progeny trials, two in the North Island of New Zealand and one in Tasmania, Australia, were available to estimate heritability between trait genetic correlations and genotype × environment interaction. Resistance to cyclaneusma needle cast had moderate estimates of heritability (0.25 to 0.46) at all sites. Genetic correlations between the assessed traits indicated that selection for faster early growth, i.e., tree height at age 4 years and diameter at breast height at age 6 years, favours trees that are prone to Cyclaneusma infection, while a favourable genetic association between resistance to cyclaneusma needle cast and productivity was evident at a later assessment at age 9 years. No significant genotype × environment interaction was found for resistance to cyclaneusma needle cast; however, stability of genotypes across a wider range of environments and with a high genetic connectedness requires more research. Considerable genetic improvement can be achieved for resistance to cyclaneusma needle cast and indirect selection for the trait should be pursued by selecting for productivity and culling susceptible genotypes from breeding.

Do stronger measures of genomic connectedness enhance prediction accuracies across management units?

Genetic connectedness assesses the extent to which estimated breeding values can be fairly compared across management units. Ranking of individuals across units based on best linear unbiased prediction (BLUP) is reliable when there is a sufficient level of connectedness due to a better disentangling of genetic signal from noise. Connectedness arises from genetic relationships among individuals. Although a recent study showed that genomic relatedness strengthens the estimates of connectedness across management units compared with that of pedigree, the relationship between connectedness measures and prediction accuracies only has been explored to a limited extent. In this study, we examined whether increased measures of connectedness led to higher prediction accuracies evaluated by a cross-validation (CV) based on computer simulations. We applied prediction error variance of the difference, coefficient of determination (CD), and BLUP-type prediction models to data simulated under various scenarios. We found that a greater extent of connectedness enhanced accuracy of whole-genome prediction. The impact of genomics was more marked when large numbers of markers were used to infer connectedness and evaluate prediction accuracy. Connectedness across units increased with the proportion of connecting individuals and this increase was associated with improved accuracy of prediction. The use of genomic information resulted in increased estimates of connectedness and improved prediction accuracies compared with those of pedigree-based models when there were enough markers to capture variation due to QTL signals.

The genetic connectedness calculated from genomic information and its effect on the accuracy of genomic prediction.

The magnitude of connectedness among management units (e.g., flocks and herds) gives a reliable estimate of genetic evaluation across these units. Traditionally, pedigree-based methods have been used to evaluate the genetic connectedness in China. However, these methods have not been able to yield a substantial outcome due to the lack of accuracy and integrity of pedigree data. Therefore, it is necessary to ascertain genetic connectedness using genomic information (i.e., genome-based genetic connectedness). Moreover, the effects of various levels of genome-based genetic connectedness on the accuracy of genomic prediction still remain poorly understood. A simulation study was performed to evaluate the genome-based genetic connectedness across herds by applying prediction error variance of difference (PEVD), coefficient of determination (CD) and prediction error correlation (r). Genomic estimated breeding values (GEBV) were predicted using a GBLUP model from a single and joint reference population. Overall, a continued increase in CD and r with a corresponding decrease in PEVD was observed as the number of common sires varies from 0 to 19 regardless of heritability levels, indicating increasing genetic connectedness between herds. Higher heritability tends to obtain stronger genetic connectedness. Compared to pedigree information, genomic relatedness inferred from genomic information increased the estimates of genetic connectedness across herds. Genomic prediction using the joint versus single reference population increased the accuracy of genomic prediction by 25% and lower heritability benefited more. Moreover, the largest benefits were observed as the number of common sires equals 0, and the gain of accuracy decreased as the number of common sires increased. We confirmed that genome-based genetic connectedness enhanced the estimates of genetic connectedness across management units. Additionally, using the combined reference population substantially increased accuracy of genomic prediction. However, care should be taken when combining reference data for closely related populations, which may give less reliable prediction results.

Evaluation of the potential use of a meta-population for genomic selection in autochthonous beef cattle populations

This study investigated the potential application of genomic selection under a multi-breed scheme in the Spanish autochthonous beef cattle populations using a simulation study that replicates the structure of linkage disequilibrium obtained from a sample of 25 triplets of sire/dam/offspring per population and using the BovineHD Beadchip. Purebred and combined reference sets were used for the genomic evaluation and several scenarios of different genetic architecture of the trait were investigated. The single-breed evaluations yielded the highest within-breed accuracies. Across breed accuracies were found low but positive on average confirming the genetic connectedness between the populations. If the same genotyping effort is split in several populations, the accuracies were lower when compared with single-breed evaluation, but showed a small advantage over small-sized purebred reference sets over the accuracies of subsequent generations. Besides, the genetic architecture of the trait did not show any relevant effect on the accuracy with the exception of rare variants, which yielded slightly lower results and higher loss of predictive ability over the generations.

Genomic Relatedness Strengthens Genetic Connectedness Across Management Units.

Genetic connectedness refers to a measure of genetic relatedness across management units (e.g., herds and flocks). With the presence of high genetic connectedness in management units, best linear unbiased prediction (BLUP) is known to provide reliable comparisons between estimated genetic values. Genetic connectedness has been studied for pedigree-based BLUP; however, relatively little attention has been paid to using genomic information to measure connectedness. In this study, we assessed genome-based connectedness across management units by applying prediction error variance of difference (PEVD), coefficient of determination (CD), and prediction error correlation r to a combination of computer simulation and real data (mice and cattle). We found that genomic information () increased the estimate of connectedness among individuals from different management units compared to that based on pedigree (). A disconnected design benefited the most. In both datasets, PEVD and CD statistics inferred increased connectedness across units when using - rather than -based relatedness, suggesting stronger connectedness. With r once using allele frequencies equal to one-half or scaling to values between 0 and 2, which is intrinsic to connectedness also increased with genomic information. However, PEVD occasionally increased, and r decreased when obtained using the alternative form of instead suggesting less connectedness. Such inconsistencies were not found with CD. We contend that genomic relatedness strengthens measures of genetic connectedness across units and has the potential to aid genomic evaluation of livestock species.

Rapid divergence of animal personality and syndrome structure across an arid-aquatic habitat matrix.

Intraspecific trait variation, including animal personalities and behavioural syndromes, affects how individual animals and populations interact with their environment. Within-species behavioural variation is widespread across animal taxa, which has substantial and unexplored implications for the ecological and evolutionary processes of animals. Accordingly, we sought to investigate individual behavioural characteristics in several populations of a desert-dwelling fish, the Australian desert goby (Chlamydogobius eremius). We reared first generation offspring in a common garden to compare non-ontogenic divergence in behavioural phenotypes between genetically interconnected populations from contrasting habitats (isolated groundwater springs versus hydrologically variable river waterholes). Despite the genetic connectedness of populations, fish had divergent bold-exploratory traits associated with their source habitat. This demonstrates divergence in risk-taking traits as a rapid phenotypic response to ecological pressures in arid aquatic habitats: neophilia may be suppressed by increased predation pressure and elevated by high intraspecific competition. Correlations between personality traits also differed between spring and river fish. River populations showed correlations between dispersal and novel environment behaviours, revealing an adaptive behavioural syndrome (related to dispersal and exploration) that was not found in spring populations. This illustrates the adaptive significance of heritable behavioural variation within and between populations, and their importance to animals persisting across contrasting habitats.

189 Genomic relatedness strengthens genetic connectedness across management units

189 Genomic relatedness strengthens genetic connectedness across management units

Estimation of genetic connectedness diagnostics based on prediction errors without the prediction error variance\u2013covariance matrix

BackgroundAn important issue in genetic evaluation is the comparability of random effects (breeding values), particularly between pairs of animals in different contemporary groups. This is usually referred to as genetic connectedness. While various measures of connectedness have been proposed in the literature, there is general agreement that the most appropriate measure is some function of the prediction error variance–covariance matrix. However, obtaining the prediction error variance–covariance matrix is computationally demanding for large-scale genetic evaluations. Many alternative statistics have been proposed that avoid the computational cost of obtaining the prediction error variance–covariance matrix, such as counts of genetic links between contemporary groups, gene flow matrices, and functions of the variance–covariance matrix of estimated contemporary group fixed effects.ResultsIn this paper, we show that a correction to the variance–covariance matrix of estimated contemporary group fixed effects will produce the exact prediction error variance–covariance matrix averaged by contemporary group for univariate models in the presence of single or multiple fixed effects and one random effect. We demonstrate the correction for a series of models and show that approximations to the prediction error matrix based solely on the variance–covariance matrix of estimated contemporary group fixed effects are inappropriate in certain circumstances.ConclusionsOur method allows for the calculation of a connectedness measure based on the prediction error variance–covariance matrix by calculating only the variance–covariance matrix of estimated fixed effects. Since the number of fixed effects in genetic evaluation is usually orders of magnitudes smaller than the number of random effect levels, the computational requirements for our method should be reduced.

Patterns of additive genotype-by-environment interaction in tree height of Norway spruce in southern and central Sweden

Genotype-by-environment (G × E) interaction for tree height measured at ages 7 to 13 was investigated in 20 large open-pollinated progeny trials for Norway spruce (Picea abies (L.) H. Karst.) in southern and central Sweden. Factor analytic method using spatially adjusted data and a reduced animal model was used to explore the pattern of G × E interaction. Extended factor analyses captured 93.0% of additive G × E interaction variances using three factors. The mean daily temperature less than 3.2 °C in May and June explained 27.8% G × E interaction, and it was moderately correlated with the first factor, indicating that spring or autumn frost weather condition could be a main driver for G × E interaction in Norway spruce. Cluster analysis has divided 20 trials into either 6 clusters or 3 clusters. Both sets of clusters reflected the geography of the trials (climates) and the genetic connectedness among testing series, indicating that more trials with better connectedness are required to examine whether current delineation of breeding or seed zones is optimal. Parental stability using latent regression could be used to locate best parents that have the highest breeding values and are highly stable across trials.

Whole genomic prediction of growth and carcass traits in a Chinese quality chicken population.

By incorporating high-density markers into breeding value prediction models, the whole genomic prediction (WGP) method can effectively accelerate genetic improvement in livestock breeding. However, the performance of WGP varies across species and populations and is affected by the underlying genetic architecture. In particular, very little is known about the performance of WGP for many chicken breeds. Here we estimate the genetic parameters and evaluate the performance of WGP for 18 growth and carcass traits in a Chinese quality chicken population. In total, 435 chickens were systematically phenotyped and genotyped using a 600K genotyping array. Two variance component estimation scenarios, 3 breeding value prediction methods, and 2 validation procedures were compared. The results showed that the heritability of these 18 traits was medium to high (ranging from 0.28 to 0.60) and that deviations existed between the heritability estimated from pedigrees and markers. Compared with conventional breeding methods, WGP could potentially increase the selection accuracy by 20% or more depending on the prediction model used, the trait under consideration, and the genetic connectedness between the training and validation individuals. Our results showed the potential of implementing genomic selection in small breeding herds.

Genetic isolation between coastal and fishery-impacted, offshore bottlenose dolphin (Tursiops spp.) populations.

The identification of species and population boundaries is important in both evolutionary and conservation biology. In recent years, new population genetic and computational methods for estimating population parameters and testing hypotheses in a quantitative manner have emerged. Using a Bayesian framework and a quantitative model-testing approach, we evaluated the species status and genetic connectedness of bottlenose dolphin (Tursiops spp.) populations off remote northwestern Australia, with a focus on pelagic 'offshore' dolphins subject to incidental capture in a trawl fishery. We analysed 71 dolphin samples from three sites beyond the 50 m depth contour (the inshore boundary of the fishery) and up to 170km offshore, including incidentally caught and free-ranging individuals associating with trawl vessels, and 273 dolphins sampled at 12 coastal sites inshore of the 50 m depth contour and within 10km of the coast. Results from 19 nuclear microsatellite markers showed significant population structure between dolphins from within the fishery and coastal sites, but also among dolphins from coastal sites, identifying three coastal populations. Moreover, we found no current or historic gene flow into the offshore population in the region of the fishery, indicating a complete lack of recruitment from coastal sites. Mitochondrial DNA corroborated our findings of genetic isolation between dolphins from the offshore population and coastal sites. Most offshore individuals formed a monophyletic clade with common bottlenose dolphins (T.truncatus), while all 273 individuals sampled coastally formed a well-supported clade of Indo-Pacific bottlenose dolphins (T.aduncus). By including a quantitative modelling approach, our study explicitly took evolutionary processes into account for informing the conservation and management of protected species. As such, it may serve as a template for other, similarly inaccessible study populations.

Can multi-subpopulation reference sets improve the genomic predictive ability for pigs?

In most countries and for most livestock species, genomic evaluations are obtained from within-breed analyses. To achieve reliable breeding values, however, a sufficient reference sample size is essential. To increase this size, the use of multibreed reference populations for small populations is considered a suitable option in other species. Over decades, the separate breeding work of different pig breeding organizations in Germany has led to stratified subpopulations in the breed German Large White. Due to this fact and the limited number of Large White animals available in each organization, there was a pressing need for ascertaining if multi-subpopulation genomic prediction is superior compared with within-subpopulation prediction in pigs. Direct genomic breeding values were estimated with genomic BLUP for the trait "number of piglets born alive" using genotype data (Illumina Porcine 60K SNP BeadChip) from 2,053 German Large White animals from five different commercial pig breeding companies. To assess the prediction accuracy of within- and multi-subpopulation reference sets, a random 5-fold cross-validation with 20 replications was performed. The five subpopulations considered were only slightly differentiated from each other. However, the prediction accuracy of the multi-subpopulations approach was not better than that of the within-subpopulation evaluation, for which the predictive ability was already high. Reference sets composed of closely related multi-subpopulation sets performed better than sets of distantly related subpopulations but not better than the within-subpopulation approach. Despite the low differentiation of the five subpopulations, the genetic connectedness between these different subpopulations seems to be too small to improve the prediction accuracy by applying multi-subpopulation reference sets. Consequently, resources should be used for enlarging the reference population within subpopulation, for example, by adding genotyped females.

Population Structure in the Roundtail Chub (Gila robusta Complex) of the Gila River Basin as Determined by Microsatellites: Evolutionary and Conservation Implications

Ten microsatellite loci were characterized for 34 locations from roundtail chub (Gila robusta complex) to better resolve patterns of genetic variation among local populations in the lower Colorado River basin. This group has had a complex taxonomic history and previous molecular analyses failed to identify species diagnostic molecular markers. Our results supported previous molecular studies based on allozymes and DNA sequences, which found that most genetic variance was explained by differences among local populations. Samples from most localities were so divergent species-level diagnostic markers were not found. Some geographic samples were discordant with current taxonomy due to admixture or misidentification; therefore, additional morphological studies are necessary. Differences in spatial genetic structure were consistent with differences in connectivity of stream habitats, with the typically mainstem species, G. robusta, exhibiting greater genetic connectedness within the Gila River drainage. No species exhibited strong isolation by distance over the entire stream network, but the two species typically found in headwaters, G. nigra and G. intermedia, exhibited greater than expected genetic similarity between geographically proximate populations, and usually clustered with individuals from the same geographic location and/or sub-basin. These results highlight the significance of microevolutionary processes and importance of maintaining local populations to maximize evolutionary potential for this complex. Augmentation stocking as a conservation management strategy should only occur under extreme circumstances, and potential source populations should be geographically proximate stocks of the same species, especially for the headwater forms.

Genetic connections between dressage and show-jumping horses in Dutch Warmblood horses

During the last decades, the breeding practice within the Dutch Warmblood studbook (KWPN) has resulted in an increasing specialisation of horses into show-jumping (JH) and dressage (DH). The objective of this study was to describe the effect of the specialisation on the connectedness between the subpopulations of JH and DH horses registered by KWPN. The subpopulations comprised 23,800 JH horses and 18,125 DH horses, born between 1995 and 2009. Genetic similarity (GS), genetic pool in common (GCx) based on the marginal genetic contribution of common ancestors and coefficient of relationship (r) between and within subpopulations were analysed in three periods of time to describe changes in genetic connectedness between subpopulations. A decline in GS (0.97–0.45), GC0.5 (0.69–0.13) and r (0.018–0.014) in the recent years was observed. Both subpopulations have a common genetic pool; however, if the specialisation process continues, it will result in two unrelated (genetic) groups.

Genetic evaluations of the German Sport Horse: Population structure and use of data from foal and mare inspections and performance tests of mares

Abstract. The aim of the study was to characterize the population of the German Sport Horse, a sub-population of the German Riding Horse, in terms of population structure and genetic parameters. Data from 26 490 horses with information from foal inspections (FI; n=17 881), broodmare inspections (BI; n=12 069) and mare performance tests (MPT; n=2 756) from the years 1990-2006 were used for analysis. A total of 21 traits as scored in the three types of performance tests were analysed. Heritability estimates for traits from FIs ranged from 0.24 ± 0.01 (conformation) to 0.50 ± 0.01 (type). For BIs estimates ranged between 0.15 ± 0.02 (forelegs) and 0.50 ± 0.02 (head). Traits evaluated in the MPT showed heritabilities between 0.18 ± 0.02 (rideability) and 0.46 ± 0.02 (trot). Genetic correlations within and across the three tests were all positive. An analysis of the structure of genetic relationships revealed that the population is influenced by different German Riding Horse sub-populations as well as by thor ough breds. The genetic connectedness within the population is of a complex structure and appeared to be sufficient for genetic analyses. Differences between the genetic pa rame ters estimated in this study for the GSH and those used in the national breeding value esti ma tion system are predominantly insignificant. These results confirm that the GSH is both adequately represented in the national system and that the population itself is a rep re sen tative part of the entire German Riding Horse population.

국내 두록종 농장간 유전적 연결성 추정

The genetic connectedness between herds is an essential requirement to make robust across-herd estimation of the breeding values of the animals. In this study, genetic connectedness between herds was evaluated by a connectedness rating method. A total of 24,971 records of days to 90 kg (D90KG) of the pigs on performance testing programs collected from six herds (labeled from 'A' to 'F') of Duroc breed along with pedigree information comprising 456,697 families were used. Results showed that a total of eight boars were used for semen exchange programs among participant farms. Herds 'A' through 'E' were found strongly connected among them. But 'F' herd was genetically connected strongly only with 'A' herd. The highest average connectedness rating was 91.7% between 'A' herd and 'C' herd. The lowest average connectedness rating was 65.1% between 'D' and 'F'. The concept of a single genetic group comprising six Duroc herds studied is meaningful due to high connectedness rates among them. Therefore, with this high genetic ties between participant Duroc farms, the more accurate genetic evaluation would be possible.

Genomic simulation for the study of data transformation efficiency in the genetic evaluation of cattle in the presence of heterogeneity

Efficiency of data transformation strategies is evaluated to correct heterogeneity among cattle in the genetic evaluation of bulls, cows and progenies. Four data structures of bovine weaning weights were simulated: herds with and without heterogeneity for means and variances, and herds with and without genetic connectedness. In the genetic evaluations, data were used in the original scale and transformed (Logarithmic, Square root, standardization and ratio by phenotypic standard deviation). The evaluated data transformation strategies were not efficient in eliminating the negative effects of heterogeneity among cattle in the genetic evaluation of bulls, cows and progenies.

Trends of the genetic connectedness measures among Nelore beef cattle herds

Validity of comparisons between expected breeding values obtained from best linear unbiased prediction procedures in genetic evaluations is dependent on genetic connectedness among herds. Different cattle breeding programmes have their own particular features that distinguish their database structure and can affect connectedness. Thus, the evolution of these programmes can also alter the connectedness measures. This study analysed the evolution of the genetic connectedness measures among Brazilian Nelore cattle herds from 1999 to 2008, using the French Criterion of Admission to the group of Connected Herds (CACO) method, based on coefficients of determination (CD) of contrasts. Genetic connectedness levels were analysed by using simple and multiple regression analyses on herd descriptors to understand their relationship and their temporal trends from the 1999-2003 to the 2004-2008 period. The results showed a high level of genetic connectedness, with CACO estimates higher than 0.4 for the majority of them. Evaluation of the last 5-year period showed only a small increase in average CACO measures compared with the first 5 years, from 0.77 to 0.80. The percentage of herds with CACO estimates lower than 0.7 decreased from 27.5% in the first period to 16.2% in the last one. The connectedness measures were correlated with percentage of progeny from connecting sires, and the artificial insemination spread among Brazilian herds in recent years. But changes in connectedness levels were shown to be more complex, and their complete explanation cannot consider only herd descriptors. They involve more comprehensive changes in the relationship matrix, which can be only fully expressed by the CD of contrasts.