Estimation Of Genetic Relationships Research Articles

KWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity.

Modern genomics techniques generate overwhelming quantities of data. Extracting population genetic variation demands computationally efficient methods to determine genetic relatedness between individuals (or “samples”) in an unbiased manner, preferably de novo. Rapid estimation of genetic relatedness directly from sequencing data has the potential to overcome reference genome bias, and to verify that individuals belong to the correct genetic lineage before conclusions are drawn using mislabelled, or misidentified samples. We present the k-mer Weighted Inner Product (kWIP), an assembly-, and alignment-free estimator of genetic similarity. kWIP combines a probabilistic data structure with a novel metric, the weighted inner product (WIP), to efficiently calculate pairwise similarity between sequencing runs from their k-mer counts. It produces a distance matrix, which can then be further analysed and visualised. Our method does not require prior knowledge of the underlying genomes and applications include establishing sample identity and detecting mix-up, non-obvious genomic variation, and population structure. We show that kWIP can reconstruct the true relatedness between samples from simulated populations. By re-analysing several published datasets we show that our results are consistent with marker-based analyses. kWIP is written in C++, licensed under the GNU GPL, and is available from https://github.com/kdmurray91/kwip.

Modelling growth curve in Moghani sheep: comparison of non-linear mixed growth models and estimation of genetic relationship between growth curve parameters

SUMMARYIn order to describe the growth curves in Iranian Moghani sheep, five non-linear mixed mathematical equations (Brody, Negative exponential, Logistic, Gompertz and von Bertalanffy) were compared. After selecting the best-fitted model based on purely statistical criteria, variance components and genetic parameters for growth curve characteristics were estimated. The data set and pedigree information used in the current study were obtained from the breeding station of Moghani sheep and included 7905 weight records of 1581 lambs from birth to 400 days of age between the years 1994 and 2012 inclusive. Each model was fitted to body weight records for all lambs, males, females, single and twin lambs using the NLMIXED procedure in SAS and the parameters were estimated. Animal was considered as subject in the models. The non-linear mixed models were examined for goodness of fit using Akaike's information criterion (AIC) and residual variance. Marginal posterior distribution of genetic parameters and variance components were estimated using the Threshold Model programme. The Gibbs sampler was run for 1 000 000 rounds and the first 200 000 rounds were discarded as a burn-in period. Logistic model provided the best fit of growth curve in males, females, singles, twins and all lambs due to the lower values of AIC and residual variance compared with other models. Posterior mean estimates of direct heritabilities for asymptotic weight (A), initial animal weight (B) and maturation rate (K) parameters of Logistic model were 0·21, 0·24 and 0·29, respectively. Also, posterior mean estimates of maternal heritabilities forA,BandKwere 0·27, 0·24 and 0·19, respectively. Estimate of correlation between direct and maternal genetic effects forA,BandKparameters were −0·33, −0·69 and −0·51, respectively. Estimates of direct genetic correlation betweenA–B,A–KandB–Kwere positive and equal to 0·19, 0·07 and 0·28, respectively. Also, maternal genetic correlations betweenA–B,A–KandB–Kwere positive and equal to 0·43, 0·34 and 0·55, respectively. In general, evaluation of different growth equations used in the current study indicated the potential of the non-linear functions to fit body weight records of Moghani sheep. Also, the results of the current study showed that improvement of growth curve parameters of Moghani sheep could be possible in selection programmes. Therefore, development of an optimal selection strategy to achieve a desired shape of growth curve through changing genetically the parameters of model would be very important.

Estimation of genetic relationship of wheat germplasm against cereal cyst nematodes using RAPD technique

Investigations were conducted at molecular level, to estimate genetic diversity among wheat germplasm (20 cultivars/lines) in relation to their response against cereal cyst nematodes Heterodera avenae, through Random Amplified Polymorphic DNA (RAPD) technique. A total of 589 bands were generated using 14 primers with an average of 28.8 bands/genotype. Maximum percentage of polymorphic loci was 92.86% for genotype TJ-83. Inferences have been made regarding bioassay and molecular characterization that the most diverse and resistant genotype against CCN was Moomal-2002 as compared to the rest of the genotypes studied and the most effective loci to screen diversity was OPA-09.

Model-free Estimation of Recent Genetic Relatedness

Genealogical inference from genetic data is essential for a variety of applications in human genetics. In genome-wide and sequencing association studies, for example, accurate inference on both recent genetic relatedness, such as family structure, and more distant genetic relatedness, such as population structure, is necessary for protection against spurious associations. Distinguishing familial relatedness from population structure with genotype data, however, is difficult because both manifest as genetic similarity through the sharing of alleles. Existing approaches for inference on recent genetic relatedness have limitations in the presence of population structure, where they either (1) make strong and simplifying assumptions about population structure, which are often untenable, or (2) require correct specification of and appropriate reference population panels for the ancestries in the sample, which might be unknown or not well defined. Here, we propose PC-Relate, a model-free approach for estimating commonly used measures of recent genetic relatedness, such as kinship coefficients and IBD sharing probabilities, in the presence of unspecified structure. PC-Relate uses principal components calculated from genome-screen data to partition genetic correlations among sampled individuals due to the sharing of recent ancestors and more distant common ancestry into two separate components, without requiring specification of the ancestral populations or reference population panels. In simulation studies with population structure, including admixture, we demonstrate that PC-Relate provides accurate estimates of genetic relatedness and improved relationship classification over widely used approaches. We further demonstrate the utility of PC-Relate in applications to three ancestrally diverse samples that vary in both size and genealogical complexity.

Compression distance can discriminate animals by genetic profile, build relationship matrices and estimate breeding values

BackgroundGenetic relatedness is currently estimated by a combination of traditional pedigree-based approaches (i.e. numerator relationship matrices, NRM) and, given the recent availability of molecular information, using marker genotypes (via genomic relationship matrices, GRM). To date, GRM are computed by genome-wide pair-wise SNP (single nucleotide polymorphism) correlations.ResultsWe describe a new estimate of genetic relatedness using the concept of normalised compression distance (NCD) that is borrowed from Information Theory. Analogous to GRM, the resultant compression relationship matrix (CRM) exploits numerical patterns in genome-wide allele order and proportion, which are known to vary systematically with relatedness. We explored properties of the CRM in two industry cattle datasets by analysing the genetic basis of yearling weight, a phenotype of moderate heritability. In both Brahman (Bos indicus) and Tropical Composite (Bos taurus by Bos indicus) populations, the clustering inferred by NCD was comparable to that based on SNP correlations using standard principal component analysis approaches. One of the versions of the CRM modestly increased the amount of explained genetic variance, slightly reduced the ‘missing heritability’ and tended to improve the prediction accuracy of breeding values in both populations when compared to both NRM and GRM. Finally, a sliding window-based application of the compression approach on these populations identified genomic regions influenced by introgression of taurine haplotypes.ConclusionsFor these two bovine populations, CRM reduced the missing heritability and increased the amount of explained genetic variation for a moderately heritable complex trait. Given that NCD can sensitively discriminate closely related individuals, we foresee CRM having possible value for estimating breeding values in highly inbred populations.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-015-0158-9) contains supplementary material, which is available to authorized users.

Genetic and epigenetic diversity among dent, waxy, and sweet corns

Maize is an important crop species that has been subjected to intensive breeding programs. Understanding the genetic diversity in maize is thus vital for crop improvement and breeding studies. We performed four different multi-allele detecting marker systems amplified fragment length polymorphism (AFLP), sequence-specific amplified polymorphism (SSAP), methylation-sensitive amplified polymorphism (MSAP), and transposon display methylation amplified polymorphism (TD-MSAP) to analyze genetic and epigenetic variation and diversity among dent, waxy, and sweet corn. The (epi) genetic diversity, (epi) genetic distance, gene flow, genetic frequency, cluster analysis, PCoA, and AMOVA analysis were calculated. Cultivar differentiation is well-established in maize, and the results suggest that not only genetic but also epigenetic variation is responsible for the differences obtained in maize cultivars. Estimates of genetic relationship were significantly correlated between the AFLP, SSAP, and MSAP datasets. The current study is the first report on the systematic comparison of TD-MSAP with the other marker systems. The genetic variation detected by TD-MSAP was higher than that calculated by AFLP, SSAP, and MSAP but was in discordance with accepted genetic relationships. These dissimilarities between TD-MSAP and other marker systems can be informative for understanding the genetic relationships between the species.

Exploring the utility of cross-laboratory RAD-sequencing datasets for phylogenetic analysis.

BackgroundRestriction site-Associated DNA sequencing (RAD-Seq) is widely applied to generate genome-wide sequence and genetic marker datasets. RAD-Seq has been extensively utilised, both at the population level and across species, for example in the construction of phylogenetic trees. However, the consistency of RAD-Seq data generated in different laboratories, and the potential use of cross-species orthologous RAD loci in the estimation of genetic relationships, have not been widely investigated. This study describes the use of SbfI RAD-Seq data for the estimation of evolutionary relationships amongst ten teleost fish species, using previously established phylogeny as a benchmark.ResultsThe number of orthologous SbfI RAD loci identified decreased with increasing evolutionary distance between the species, with several thousand loci conserved across five salmonid species (divergence ~50 MY), and several hundred conserved across the more distantly related teleost species (divergence ~100–360 MY). The majority (>70%) of loci identified between the more distantly related species were genic in origin, suggesting that the bias of SbfI towards genic regions is useful for identifying distant orthologs. Interspecific single nucleotide variants at each orthologous RAD locus were identified. Evolutionary relationships estimated using concatenated sequences of interspecific variants were congruent with previously published phylogenies, even for distantly (divergence up to ~360 MY) related species.ConclusionOverall, this study has demonstrated that orthologous SbfI RAD loci can be identified across closely and distantly related species. This has positive implications for the repeatability of SbfI RAD-Seq and its potential to address research questions beyond the scope of the original studies. Furthermore, the concordance in tree topologies and relationships estimated in this study with published teleost phylogenies suggests that similar meta-datasets could be utilised in the prediction of evolutionary relationships across populations and species with readily available RAD-Seq datasets, but for which relationships remain uncharacterised.Electronic supplementary materialThe online version of this article (doi:10.1186/s13104-015-1261-2) contains supplementary material, which is available to authorized users.

Estimation of Genetic Relationships Between Individuals Across Cohorts and Platforms: Application to Childhood Height.

Combining genotype data across cohorts increases power to estimate the heritability due to common single nucleotide polymorphisms (SNPs), based on analyzing a Genetic Relationship Matrix (GRM). However, the combination of SNP data across multiple cohorts may lead to stratification, when for example, different genotyping platforms are used. In the current study, we address issues of combining SNP data from different cohorts, the Netherlands Twin Register (NTR) and the Generation R (GENR) study. Both cohorts include children of Northern European Dutch background (N = 3102 + 2826, respectively) who were genotyped on different platforms. We explore imputation and phasing as a tool and compare three GRM-building strategies, when data from two cohorts are (1) just combined, (2) pre-combined and cross-platform imputed and (3) cross-platform imputed and post-combined. We test these three strategies with data on childhood height for unrelated individuals (N = 3124, average age 6.7 years) to explore their effect on SNP-heritability estimates and compare results to those obtained from the independent studies. All combination strategies result in SNP-heritability estimates with a standard error smaller than those of the independent studies. We did not observe significant difference in estimates of SNP-heritability based on various cross-platform imputed GRMs. SNP-heritability of childhood height was on average estimated as 0.50 (SE = 0.10). Introducing cohort as a covariate resulted in ≈2 % drop. Principal components (PCs) adjustment resulted in SNP-heritability estimates of about 0.39 (SE = 0.11). Strikingly, we did not find significant difference between cross-platform imputed and combined GRMs. All estimates were significant regardless the use of PCs adjustment. Based on these analyses we conclude that imputation with a reference set helps to increase power to estimate SNP-heritability by combining cohorts of the same ethnicity genotyped on different platforms. However, important factors should be taken into account such as remaining cohort stratification after imputation and/or phenotypic heterogeneity between and within cohorts. Whether one should use imputation, or just combine the genotype data, depends on the number of overlapping SNPs in relation to the total number of genotyped SNPs for both cohorts, and their ability to tag all the genetic variance related to the specific trait of interest.

Estimation of genetic relationships between growth curve parameters in Guilan sheep.

The objective of this study was to estimate variance components and genetic parameters for growth curve parameters in Guilan sheep. Studied traits were parameters of Brody growth model which included A (asymptotic mature weight), B (initial animal weight) and K (maturation rate). The data set and pedigree information used in this study were obtained from the Agricultural Organization of Guilan province (Rasht, Iran) and comprised 8647 growth curve records of lambs from birth to 240 days of age during 1994 to 2014. Marginal posterior distributions of parameters and variance components were estimated using TM program. The Gibbs sampler was run 300000 rounds and the first 60000 rounds were discarded as a burn-in period. Posterior mean estimates of direct heritabilities for A, B and K were 0.39, 0.23 and 0.039, respectively. Estimates of direct genetic correlation between growth curve parameters were 0.57, 0.03 and −0.01 between A-B, A-K and B-K, respectively. Estimates of direct genetic trends for A, B and K were positive and their corresponding values were 0.014 ± 0.003 (P < 0.001), 0.0012 ± 0.0009 (P > 0.05) and 0.000002 ± 0.0001 (P > 0.05), respectively. Residual correlations between growth curve parameters varied form −0.52 (between A-K) to 0.48 (between A-B). Also, phenotypic correlations between growth curve parameters varied form −0.49 (between A-K) to 0.47 (between A-B). The results of this study indicated that improvement of growth curve parameters of Guilan sheep seems feasible in selection programs. It is worthwhile to develop a selection strategy to obtain an appropriate shape of growth curve through changing genetically the parameters of growth model.

Nest suitability, fine-scale population structure and male-mediated dispersal of a solitary ground nesting bee in an urban landscape.

Bees are the primary pollinators of flowering plants in almost all ecosystems. Worldwide declines in bee populations have raised awareness about the importance of their ecological role in maintaining ecosystem functioning. The naturally strong philopatric behavior that some bee species show can be detrimental to population viability through increased probability of inbreeding. Furthermore, bee populations found in human-altered landscapes, such as urban areas, can experience lower levels of gene flow and effective population sizes, increasing potential for inbreeding depression in wild bee populations. In this study, we investigated the fine-scale population structure of the solitary bee Colletes inaequalis in an urbanized landscape. First, we developed a predictive spatial model to detect suitable nesting habitat for this ground nesting bee and to inform our field search for nests. We genotyped 18 microsatellites in 548 female individuals collected from nest aggregations throughout the study area. Genetic relatedness estimates revealed that genetic similarity among individuals was slightly greater within nest aggregations than among randomly chosen individuals. However, genetic structure among nest aggregations was low (Nei’s GST = 0.011). Reconstruction of parental genotypes revealed greater genetic relatedness among females than among males within nest aggregations, suggesting male-mediated dispersal as a potentially important mechanism of population connectivity and inbreeding avoidance. Size of nesting patch was positively correlated with effective population size, but not with other estimators of genetic diversity. We detected a positive trend between geographic distance and genetic differentiation between nest aggregations. Our landscape genetic models suggest that increased urbanization is likely associated with higher levels of inbreeding. Overall, these findings emphasize the importance of density and distribution of suitable nesting patches for enhancing bee population abundance and connectivity in human dominated habitats and highlights the critical contribution of landscape genetic studies for enhanced conservation and management of native pollinators.

Estimation of genetic relatedness among cultivated and wild lens based on morphological and molecular markers

Lentil is an important rainfed legume grown in the winter season. Low productivity due to its narrow genetic base is the cause for concern. The objective of this study was to analyze the genetic diversity in sixty cultivated lentil genotypes based on yield and other agronomic traits. The studied genotypes were grouped in three clusters. Hundred seed weight, plant height and number of secondary branches contributed 26.98%, 17.88% and 15.95% respectively towards the genetic diversity. Intercluster distance revealed narrow genetic base of cultivated lentil. The 60 cultivated genotypes alongwith 23 wild types were also characterized using molecular markers. Dendrogram based on Jaccard similarity coefficient and UPGMA analysis revealed two major clusters and one minor cluster. Twenty-one wild accessions of L. orientalis and 1 L . e rvoides subspecies grouped separately into cluster 1. Nineteen Indian varieties grouped together in subcluster IIA indicating their narrow genetic base. Subcluster IIB consisted of 41 genotypes including 5 exotic and 36 advanced breeding lines due to use of exotic lines into recent breeding programmes. Therefore it is implied from this study that prebreeding of lentil is very essential using wild spp and exotic collection in hybridization programme, which is required for broadening of the genetic base and introgression of useful traits.

Genetic diversity assessment and estimation of phylogenetic relationships among 26 Fagaceae species using ISSRs

The family Fagaceae includes several species and presents huge genetic variability. In the last two decades, several genetic studies about phylogenetics and genetic diversity of Fagaceae have emerged. ISSR markers were used to evaluate the genetic diversity of 26 species of Fagaceae belonging to the genera Castanea, Fagus and Quercus. Among several primers tested, 17 were selected for the evaluation of diversity and estimation of genetic relationships. A total of 371 ISSR markers were produced and each primer revealed high polymorphism. Specific ISSR markers for the Quercus infrageneric groups were amplified. ISSRs proved to be a reliable tool for the discrimination of the analyzed species per genus, infrageneric group and/or ecological origin.

Testing the key assumption of heritability estimates based on genome-wide genetic relatedness

Comparing genetic and phenotypic similarity among unrelated individuals seems a promising way to quantify the genetic component of traits while avoiding the problematic assumptions plaguing twin- and other kin-based estimates of heritability. One approach uses a Genetic Relatedness Estimation through Maximum Likelihood (GREML) model for individuals who are related at less than 0.025 to predict their phenotypic similarity by their genetic similarity. Here we test the key underlying assumption of this approach: that genetic relatedness is orthogonal to environmental similarity. Using data from the Health and Retirement Study (and two other surveys), we show two unrelated individuals may be more likely to have been reared in a similar environment (urban versus nonurban setting) if they are genetically similar. This effect is not eliminated by controls for population structure. However, when we include this environmental confound in GREML models, heritabilities do not change substantially and thus potential bias in estimates of most biological phenotypes is probably minimal.

Estimation of genetic relationships among 39 cultivars of avocado (Persea americana Mill.) by analysing the volatile constituents of leaves

SummaryThe volatile constituents of leaf samples were analysed to determine genetic relationships among 39 avocado (Persea americana Mill.) cultivars (25 from Taiwan and 14 from El Salvador) representing all three horticultural races (Mexican, Gutemalan, and West-Indian). A stable isotope, internal standard-based, solid-phase micro-extraction (SPME) GC-MS method was used to provide calibrated, quantitative measures of the concentrations and compositions of volatile organic compounds (VOCs) in avocado leaves in heated headspace vials. The calibrated intensity of VOCs in the leaves of Mexican race avocados was higher than in the Guatemalan and West-Indian races. Twelve race-specific VOCs, and ten VOCs of variable abundance were selected as indicators for further analysis. A similarity matrix of VOCs was calculated using Euclidean distances of the log10 values of the calibrated abundances of the indicator compounds. A dendrogram was produced based on the unweighted pair group method using arithmetic averages (UPGMA). The 39 avocado cultivars clustered into three major groups based on their VOCs. Thirteen Taiwanese cultivars and three West-Indian cultivars were clustered in the same group in the dendrogram. The results showed that most Taiwanese cultivars were closely related to cultivars of the West-Indian race.

Studies on efficiency of RAPD primers in developing molecular profiles for genetic purity studies in soybean (Glycine max L.) cultivars

Major advances have recently been made in our understanding of soybean genetics and of the application of new technologies to soybean improvement. Estimates of genetic relationships on the basis of the enzymes and molecular markers have been shown to be consistent with expectations based on origin and pedigree information. To identify efficient markers, that are to be used for genetic purity studies, polymorphism is the basic criterion. RAPD has been found to be an effective and efficient tool to evaluate and reveal genetic polymorphism in several crop species. In present study a total of 80 RAPD primers were screened, out of which 37 gave amplification and only 30 primers showed unambiguous DNA profile. Out of these 30 primers, 22 gave polymorphic banding patterns. It is evident from the result that, 30/80 primers tried (38%) provided unambiguous amplification and out of 30 primers, 22 primers (73%) were found to be polymorphic. Scorable 30 RAPD primers led to amplification of 120 fragments out of which 81 (67.5%) bands were found to be polymorphic. On an average, we got 4 bands per primer and 15 primers (50%) have been found to produce more number of bands than the average value which is encouraging. 8 primers were found to give 100% polymorphisms. Our results are indicative of the efficiency of RAPD primers towards development of molecular profiles.

Population Genetics, Dispersal, and Kinship Among Wild Squirrel Monkeys (Saimiri sciureus macrodon): Preferential Association Between Closely Related Females and Its Implications for Insect Prey Capture Success

Little genetic information is available to evaluate hypotheses concerning the parameters that affect population genetic structure in primate taxa that exhibit interspecific variation in social systems, such as squirrel monkeys (Saimiri). Here, we used genetic data to assess dispersal patterns, kin structure, and preferential association with same-sex kin in a wild population of Saimiri sciureus macrodon. We also analyzed behavioral data to assess whether individuals that maintain shorter interindividual distances show increased insect foraging success. If there was greater male than female dispersal, then we expected mean pairwise relatedness, F ST values, and intragroup mean corrected assignment indices to be greater among adult females than among adult males. We also expected matrices of pairwise affinity indices (PAIs) for “association” (time spent ≤5 m) and “proximity” (time spent ≤10 m) among female dyads to positively correlate with a matrix of female pairwise relatedness. Not only did we find support for female philopatry, but we also found significant positive relationships between the relatedness matrix and each of the PAI matrices: females were more likely to be associated with (and proximal to) close female relatives than more distant relatives or unrelated individuals. Foraging analyses revealed that females had higher insect capture rates than males, and this sex difference may be related to a smaller mean interindividual distance among closely related female group members. Our result shows how estimates of genetic relatedness are useful for testing predictions regarding the evolution of sex-biased dispersal patterns, as well as potential relationships between kin-biased social behaviors and foraging success.

The genetic relatedness analysis of male sterile and their maintainer lines of onion (Allium cepa L.) by using RAPD primers

RAPD markers analysis was performed to investigate genetic relatedness among nine sterile (A), maintainer lines (B), and male parents (C) of onion. Initially, 180 arbitrary decamer primers were screened; of these 20 primers were selected which yielded 812 bands, 45.34% of which were found to be polymorphic. Squared-Euclidean Distance matrix revealed a minimum genetic distance between the genotypes MS 48A and MF 65C and a maximum genetic distance between the genotypes MLT 84C and MF 65B. Cluster analysis grouped the nine onion genotypes into two major clusters. The first cluster consisted of two male sterile groups, i.e. MS-65 (Arka Lalima) and MS-48 (Arka Kirthiman) of single bulb onions. The second cluster consists of MLT (Multiplier) group. PCA re-confirmed the results of the dendrogram, revealing the precision in estimation of genetic relatedness among the genotypes tested. None of the primers produced unique banding patterns to distinguish all nine genotypes. This information about genetic relatedness among the nine genotypes would be better utilized in further onion breeding programs.

Genetic admixture in pig population observed by microsatellite markers

Abstract. The aim of presented study was estimation of genetic relationship within and between 3 mentioned pig breeds bred in the Slovak Republic. Genetic variability at 10 microsatellite loci (SW24, SO107, SO068, SW936, sw353, so386, so355, sw72, tnfb, and SO070) was analysed in 412 pigs of Landrace, Yorkshire and Slovak White Improved breeds. Variation amount of each population was measured with average number of alleles per locus, heterozygosities, polymorphism information content (PIC) value were calculated. Phylogenetic trees were constructed by UPGMA. The average number of alleles per locus was 11.5, ranging from 7 (SW72) to 16 (SO068). The Slovak White Improved, Landrace and Yorkshire pig breeds showed out high degree of genetic diversity with mean expected heterozygosities of 0.720, 0.697 and 0.705 respectively. Genetic distance ranged from 0.060 between Yorkshire and Slovak White Improved to 0.203 between Landrace and Slovak White Improved breeds. The scatter diagram from principal component displayed genetic differentiation among all three breeds. A Bayesian method was applied for individual assigning testing. On the base of our results the group of Slovak White Improved population was strongly mixed with Yorkshire breed and the group of all Landrace individuals was presented as enclosed population.

Genomic tools for the analysis of genetic diversity

We now understand that many different types of DNA structural polymorphisms contribute to functional diversity of plant genomes, including single nucleotide polymorphisms, insertions of retrotransposons and DNA transposons, including Helitrons carrying pseudogenes, and other types of insertion–deletion polymorphisms, many of which may contribute to the phenotype by affecting gene expression through a variety of mechanisms including those involving non-coding RNAs. These polymorphisms can now be probed with tools such as array comparative genomic hybridization and, most comprehensively, genomic sequencing. Rapid developments in next generation sequencing will soon make genomic sequencing of germplasm collections a reality. This will help eliminate an important difficulty in the estimation of genetic relationships between accessions caused by ascertainment bias. Also, it has now become obvious that epigenetic differences, such as cytosine methylation, also contribute to the heritable phenotype, although detailed understanding of their transgenerational stability in crop species is lacking. The degree of linkage disequilibrium of epialleles with DNA sequence polymorphisms has important implications to the analysis of genetic diversity. Epigenetic marks in complete linkage disequilibrium (LD) with DNA polymorphisms do not add additional diversity information. However, epialleles in partial or low LD with DNA sequence alleles constitute another layer of genetic information that should not be neglected in germplasm analysis, especially if they exhibit transgenerational stability.

Kinship affects investment by helpers in a cooperatively breeding bird

Helping behaviour in cooperative breeding systems has been attributed to kin selection, but the relative roles of direct and indirect fitness benefits in the evolution of such systems remain a matter of debate. In theory, helpers could maximize the indirect fitness benefits of cooperation by investing more in broods with whom they are more closely related, but there is little evidence for such fine-scale adjustment in helper effort among cooperative vertebrates. In this study, we used the unusual cooperative breeding system of the long-tailed tit Aegithalos caudatus to test the hypothesis that the provisioning effort of helpers was positively correlated with their kinship to broods. We first use pedigrees and microsatellite genotypes to characterize the relatedness between helpers and breeders from a 14 year field study. We used both pedigree and genetic approaches because long-tailed tits have access to pedigree information acquired through social relationships, but any fitness consequences will be determined by genetic relatedness. We then show using both pedigrees and genetic relatedness estimates that alloparental investment by helpers increases as their relatedness to the recipients of their care increases. We conclude that kin selection has played a critical role in moulding the investment decisions of helpers in this cooperatively breeding species.