FecalSeq enrichment with RAD Sequencing from non-invasive environmental samples holds promise for genetic monitoring of an imperiled lagomorph

Despite advances in genomic sequencing and bioinformatics, conservation genomics is still often hindered by a reliance on non-invasive samples. The presence of exogenous DNA and the low quantity and poor quality of DNA in non-invasive samples have been a roadblock to sequencing, thereby limiting the potential for genomic monitoring of endangered species. Recent molecular advances, such as host DNA enrichment, hold promise for facilitating sequencing from non-invasive samples. We used the FecalSeq method to enrich DNA extracted from wild-collected fecal pellets of the imperiled New England cottontail and identified SNPs from 3RAD Sequencing. We obtained SNPs from rabbit pellets, including pellets that were collected in poor environmental conditions and samples that performed poorly with microsatellites. Measures of sequencing success improved with greater amounts of starting DNA and 32% of samples generated SNP genotypes that passed quality control filtering. Genotyping error rates were high, however, and the approach was unable to consistently distinguish unique individuals or matching genotypes, while it was suitable for recovering the expected population structure. Pairing FecalSeq enrichment with RADseq is a promising low-cost method for monitoring wild populations using non-invasive samples in an environmental context, but it may be better suited for informing conservation through population genomics.

Thirty years of conservation breeding: Assessing the genetic diversity of captive Livingstone's fruit bats

Fruit bats (genus Pteropus) are typically island-endemic species important in seed dispersal and reforestation that are vulnerable to increased extinction risk. An effective method of reducing extinction risk in vulnerable species that cannot be conserved in their native habitat is establishing an ex-situ captive breeding programme. Due to anthropogenic threats and low population numbers, in the early 1990s, a captive breeding programme was established at Jersey Zoo, British Isles, for Critically Endangered Livingstone's fruit bats (Pteropus livingstonii). Here we use six polymorphic microsatellite loci to assess genetic diversity in the captive breeding population of Livingstone's fruit bats (P. livingstonii), 30 years after the programme's establishment, investigating change over generations and comparing our findings with published data from the wild population. We found no significant difference between the genetic diversity in the captive and wild populations of Livingstone's fruit bats (P. livingstonii), in both expected heterozygosity and allelic richness. The captive population has retained a comparable level of genetic diversity to that documented in the wild, and there has been no significant decline in genetic diversity over the last 30 years. We advise that a full pedigree of the paternal lineage is created to improve the management of the captive breeding programme and further reduce the possibility of inbreeding. However, it appears that the captive breeding programme is currently effective at maintaining genetic diversity at levels comparable to those seen in the wild population, which suggests reintroductions could be viable if genetic diversity remains stable in captivity.

Computing linkage disequilibrium aware genome embeddings using autoencoders

MOTIVATION

The completion of the genome has paved the way for genome-wide association studies (GWAS), which explained certain proportions of heritability. GWAS are not optimally suited to detect non-linear effects in disease risk, possibly hidden in non-additive interactions (epistasis). Alternative methods for epistasis detection using, e.g. deep neural networks (DNNs) are currently under active development. However, DNNs are constrained by finite computational resources, which can be rapidly depleted due to increasing complexity with the sheer size of the genome. Besides, the curse of dimensionality complicates the task of capturing meaningful genetic patterns for DNNs; therefore necessitates dimensionality reduction.

RESULTS

We propose a method to compress single nucleotide polymorphism (SNP) data, while leveraging the linkage disequilibrium (LD) structure and preserving potential epistasis. This method involves clustering correlated SNPs into haplotype blocks and training per-block autoencoders to learn a compressed representation of the block's genetic content. We provide an adjustable autoencoder design to accommodate diverse blocks and bypass extensive hyperparameter tuning. We applied this method to genotyping data from Project MinE, and achieved 99% average test reconstruction accuracy-i.e. minimal information loss-while compressing the input to nearly 10% of the original size. We demonstrate that haplotype-block based autoencoders outperform linear Principal Component Analysis (PCA) by approximately 3% chromosome-wide accuracy of reconstructed variants. To the extent of our knowledge, our approach is the first to simultaneously leverage haplotype structure and DNNs for dimensionality reduction of genetic data.

AVAILABILITY AND IMPLEMENTATION

Data are available for academic use through Project MinE at https://www.projectmine.com/research/data-sharing/, contingent upon terms and requirements specified by the source studies. Code is available at https://github.com/gizem-tas/haploblock-autoencoders.

Genetic structure and origin of emu populations in Japanese farms inferred from large-scale SNP genotyping based on double-digest RAD-seq

The emu is a novel poultry species in Japan. However, Japanese farmed emu populations have reduced genetic diversity owing to inbreeding. We have previously suggested that there are genetic resources in the Tohoku Safari Park (TSP) and Fuji/Kakegawa Kachoen Garden Park (FGP/KGP) to extend the genetic diversity of commercial emu farms based on microsatellite (SSR) and mitochondrial DNA. However, those markers provide relatively poor information. Thus, we investigated the genetic structure of farmed Japanese populations based on a large-scale genotyping system using RAD-seq and verified the usefulness of TSP and FGP/KGP as genetic resources for expanding genetic diversity. Admixture, phylogenetic, and principal component analyses based on 28,676 SNPs showed that TSP individuals were ancestors in the Okhotsk Emu Farm (OEF). FGP/KGP individuals showed a unique genetic component that differed from that of the others. We have previously reported that the mitochondrial haplotypes of FGP/KGP were shared with an isolated wild population in eastern Australia. These results suggest that FGP/KGP individuals originated from an eastern Australia isolated population different from other populations including ancestral of OEF/TSP. Our results would provide information for the development of Japanese emu farms and industry and for the conservation of genetic resources in the Australian wild emu.

Toll-like receptor 9 (-1237 T/C, -1486 T/C) and the risk of gastric cancer: a meta-analysis of genetic association studies

BACKGROUND

Gastric cancer has a complex aetiology including genetic factors. Individual case-control studies of toll like receptor (TLR) 9 (-1237 T/C, -1486 T/C) polymorphisms in the gastric cancer risk were available, and they showed variation in the findings. Therefore, we performed a meta-analysis to synthesize the evidence on the association between polymorphisms of TLR 9 (-1237 T/C, -1486 T/C) and the risk of gastric cancer using data from eligible studies.

METHODS

This study followed the PRISMA 2020 Checklist. Studies were searched in health-related databases. The methodological quality of studies was evaluated with the use of Newcastle-Ottawa Scale criteria. The summary odds ratio (OR) and its 95% confidence interval (CI) were used to determine the strength of association between each polymorphism and the risk of gastric cancer using five genetic models. Stratification was done by ethnic groups. For the robustness of the analysis, a leave-one-out meta-analysis was performed.

RESULTS

Eight case-control studies with 3,644 participants (1914 cases, 1730 controls) were conducted across six countries. Half of the studies were conducted in China. In the NOS methodological quality assessment, only three studies received a high-quality rating (i.e., a score of ≥ 7). TLR 9 (-1486 T/C) polymorphism and the risk of gastric cancer were assessed in six studies, four of Asian ethnicity and two of non-Asian. Under the dominant model, only in the Asian ethnic group showed a marginally and significantly increased risk of gastric cancer (overall: OR = 1.22, 95%CI = 0.90-1.67, I2 = 56%; Asian: OR = 1.24, 95%CI = 1.00-1.54, I2 = 0%, non-Asian: OR = 1.25, 95%CI = 0.38-4.09, I2 = 89%). Under the recessive model in the absence of heterogeneity, only the Asian group had a significantly higher risk of developing gastric cancer (overall: OR = 1.4, 95% CI = 0.74-2.64, I2 = 85%; Asian: OR: 1.41, 95% CI = 1.07-1.86, I2 = 0%, non-Asian: OR = 1.18, 95% CI = 0.12-11.76, I2 = 97%). Under the heterozygous model, there was no significant association with the risk of gastric cancer overall or among any ethnic subgroup. Under the homozygous model in the absence of heterogeneity, only the Asian group had a significantly higher risk of gastric cancer (overall, OR = 1.47, 95% CI = 0.76-2.86, I2 = 82%; Asian: OR = 1.54, 95% CI = 1.13-2.1, I2 = 0%; non-Asian: OR = 1.19, 95% CI = 0.1-14.33, I2 = 96%). Under the allele model, a significantly increased risk of gastric cancer was observed only in the Asian group (overall: OR = 1.23, 95% CI = 0.89-1.71, I2 = 84%; Asian: OR = 1.22, 95% CI = 1.05-1.41, I2 = 0%; non-Asian: OR = 1.24, 95% CI = 0.34-4.59, I2 = 97%). Four studies investigated the association between TLR 9 (-1237 T/C) polymorphism and the risk of developing gastric cancer. Under any of the five genetic models, there was no association between TLR 9 (-1237 T/C) and the development of gastric cancer in overall or in any ethnic subgroup. Sensitivity analysis revealed that the effect was unstable. With a small number of studies with a small number of participants, we addressed the issue of insufficient power for drawing conclusions.

CONCLUSIONS

The findings suggested that TLR9 (-1486 T/C) may play a role in the risk of gastric cancer specific to the Asian ethnic group. To substantiate the findings on the association between these two polymorphisms (TLR9 -1237 T/C, -1486 T/C) and the risk of gastric cancer, future well-designed case-control studies with a sufficient number of participants in multi-ethnic groups are recommended.

Male reproductive success is not strongly affected by phenological changes in mate availability in monoecious Sagittaria latifolia

Many plants express their female and male sex roles at different times (dichogamy), with important consequences for mating. Dichogamy can yield mate limitation via biased floral sex ratios, particularly at the beginning and end of the flowering season when many plants simultaneously function as the same sex. This form of mate limitation should be reduced if plants adjust their allocations to female versus male sex functions in a manner that tracks seasonal variability in mating opportunities. For example, under protogyny (i.e. dichogamy with female function expressed first) plants with male-biased sex expression should have enhanced mating opportunities early in the flowering season as other plants begin to flower (in female sex phase). We quantified seasonal changes in sex allocation, patterns of mate availability and realized siring success in a population of protogynous Sagittaria latifolia. Our results were consistent with previous findings that seasonal changes in sex allocation should compensate for lost mating opportunities under the temporally variable mating environments caused by dichogamy. However, patterns of siring success in the population were inconsistent with this interpretation. We suggest that realized siring success might depend more strongly on spatial than on temporal aspects of mate availability.

Understanding Mendelian errors in SNP arrays data using a Gochu Asturcelta pig pedigree: genomic alterations, family size and calling errors

Up to 478 Gochu Asturcelta pig parents-offspring trios (61 different families) were genotyped using the Axiom_PigHDv1 Array to identify the causes of Mendelian errors (ME). Up to 545,364 SNPs were retained. Up to 40,540 SNPs gathering 292,297 allelic mismatches were identified and were overlapped with SINEs and LINEs (Sscrofa genome 11.1). Copy number variations (CNV) were called using PennCNV. ME were classified into eight different classes according to the trio member ("Trio" meaning no assignment) and the allele on which ME was identified: TrioA/B, FatherA/B, MotherA/B, OffspringA/B. Most ME occurred due to systematic causes: (a) those assigned to the Father, Mother or Offspring occurred by null or partial null alleles characterized by heterozygote deficiency, varied with family size, involved a low number of loci (6506), and gathered most mismatches (228,145); (b) TrioB errors varied with family size, covaried with SINEs, LINEs and CNV, and involved most ME loci (33,483) and mismatches (65,682); and (c) TrioA errors were non-systematic ME with no sampling bias involving 1.2% of mismatches only and a low number of loci (1939). The influence of TrioB errors on the overall genotyping quality may be low and, since CNV vary among populations, their removal should be considered in each particular dataset. ME assignable to the Father, Mother or Offspring may be consistent within technological platforms and may bias severely linkage or association studies. Most ME caused by null or partial null alleles can be removed using heterozygote deficiency without affecting the size of the datasets.

Sexual selection on male but not female function in monoecious and dioecious populations of broadleaf arrowhead (Sagittaria latifolia)

Direct measures of sexual selection in plants are rare and complicated by immobility and modular growth. For plants, instantaneous measures of fitness typically scale with size, but covariances between size and mating success could obscure the detection of sexual selection. We measured the magnitude of sexual selection in a monoecious and a dioecious population of the clonal plant Sagittaria latifolia using Bateman gradients (ßss). These gradients were calculated using parentage analysis and residual regression to account for the effects of shoot and clone size on mating and reproductive success. In both populations, (i) there was greater promiscuity via male function than via female function and (ii) ßss were positive, with significant associations between mating and reproductive success for male but not female function. Moreover, estimated βss were similar for the monoecious and dioecious populations, possibly because non-overlapping female and male sex phases in hermaphroditic S. latifolia reduced the scope for interference between sex functions during mating. This study builds on previous studies of selection on plant mating traits, and of sexual selection under experimental conditions, by showing that sexual selection can operate in natural populations of plants, including populations of hermaphrodites.

Temporal sampling and network analysis reveal rapid population turnover and dynamic migration pattern in overwintering regions of a cosmopolitan pest

Genetic makeup of insect pest is informative for source-sink dynamics, spreading of insecticide resistant genes, and effective management. However, collecting samples from field populations without considering temporal resolution and calculating parameters related to historical gene flow may not capture contemporary genetic pattern and metapopulation dynamics of highly dispersive pests. Plutella xylostella (L.), the most widely distributed Lepidopteran pest that developed resistance to almost all current insecticides, migrates heterogeneously across space and time. To investigate its real-time genetic pattern and dynamics, we executed four samplings over two consecutive years across Southern China and Southeast Asia, and constructed population network based on contemporary gene flow. Across 48 populations, genetic structure analysis identified two differentiated insect swarms, of which the one with higher genetic variation was replaced by the other over time. We further inferred gene flow by estimation of kinship relationship and constructed migration network in each sampling time. Interestingly, we found mean migration distance at around 1,000 km. Such distance might have contributed to the formation of step-stone migration and migration circuit over large geographical scale. Probing network clustering across sampling times, we found a dynamic P. xylostella metapopulation with more active migration in spring than in winter, and identified a consistent pattern that some regions are sources (e.g., Yunnan in China, Myanmar and Vietnam) while several others are sinks (e.g., Guangdong and Fujian in China) over 2 years. Rapid turnover of insect swarms and highly dynamic metapopulation highlight the importance of temporal sampling and network analysis in investigation of source-sink relationships and thus effective pest management of P. xylostella, and other highly dispersive insect pests.

Evaluating sources of bias in pedigree-based estimates of breeding population size

Applications of genetic-based estimates of population size are expanding, especially for species for which traditional demographic estimation methods are intractable due to the rarity of adult encounters. Estimates of breeding population size (N_S ) are particularly amenable to genetic-based approaches as the parameter can be estimated using pedigrees reconstructed from genetic data gathered from discrete juvenile cohorts, therefore eliminating the need to sample adults in the population. However, a critical evaluation of how genotyping and sampling effort influence bias in pedigree reconstruction, and how these biases subsequently influence estimates of N_S , is needed to evaluate the efficacy of the approach under a range of scenarios. We simulated a model system to understand the interactive effects of genotyping and sampling effort on error in genetic pedigrees reconstructed from the program COLONY. We then evaluated how errors in pedigree reconstruction influenced bias and precision in estimates of N_S using three different rarefaction estimators. Results indicated that pedigree error can be minimal when adequate genetic data are available, such as when juvenile sample sizes are large and/or individuals are genotyped at many informative loci. However, even in cases for which data are limited, using results of the simulation analysis to understand the magnitude and sources of bias in reconstructed pedigrees can still be informative when estimating N_S . We applied results of the simulation analysis to evaluate N ̂ $$ \hat{N} $$ _S for a population of federally endangered Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus) in the Delaware River, USA. Our results indicated that N_S is likely to be three orders of magnitude lower compared with historic breeding population sizes, which is a considerable advancement in our understanding of the population status of Atlantic sturgeon in the Delaware River. Our analyses are broadly applicable in the design and interpretation of studies seeking to estimate N_S and can help to guide conservation decisions when ecological uncertainty is high. The utility of these results is expected to grow as rapid advances in genetic technologies increase the popularity of genetic population monitoring and estimation.

Assessing Population Genetic Status for Designing Plant Translocations

Assisted gene flow interventions such as plant translocations are valuable complementary techniques to habitat restoration. Bringing new genetic variants can contribute to increasing genetic diversity and evolutionary resilience, counteract inbreeding depression and improve plant fitness through heterosis. Large, highly genetically variable populations are usually recommended as sources for translocation. Unfortunately, many critically endangered species only occur as small populations, which are expected to show low genetic variation, high inbreeding level, paucity of compatible mates in self-incompatible species, and increased genetic divergence. Therefore, assessment of population genetic status is required for an appropriate choice of the source populations. In this paper, we exemplify the different analyses relevant for genetic evaluation of populations combining both molecular (plastid and nuclear) markers and fitness-related quantitative traits. We assessed the genetic status of the adult generation and their seed progeny (the potential translocation founders) of small populations of Campanula glomerata (Campanulaceae), a self-incompatible insect-pollinated herbaceous species critically endangered in Belgium. Only a few small populations remain, so that the species has been part of a restoration project of calcareous grasslands implementing plant translocations. In particular, we estimated genetic diversity, inbreeding levels, genetic structure in adults and their seed progeny, recent bottlenecks, clonal extent in adults, contemporary gene flow, effective population size (Ne), and parentage, sibship and seed progeny fitness variation. Small populations of C. glomerata presented high genetic diversity, and extensive contemporary pollen flow within populations, with multiple parentage among seed progenies, and so could be good seed source candidates for translocations. As populations are differentiated from each other, mixing the sources will not only optimize the number of variants and of compatible mates in translocated populations, but also representativeness of species regional genetic diversity. Genetic diversity is no immediate threat to population persistence, but small Ne, restricted among-population gene flow, and evidence of processes leading to genetic erosion, inbreeding and inbreeding depression in the seed progeny require management measures to counteract these trends and stochastic vulnerability. Habitat restoration facilitating recruitment, flowering and pollination, reconnecting populations by biological corridors or stepping stones, and creating new populations through translocations in protected areas are particularly recommended.

Performance comparison of gel and capillary electrophoresis-based microsatellite genotyping strategies in a population research and kinship testing framework

OBJECTIVE

The advancement of molecular techniques in an era in which high-throughput sequencing has revolutionized biology renders old-fashioned alternatives to high-throughput methods obsolete. Such advanced molecular techniques, however, are not yet accessible to economically disadvantaged region-based laboratories that still obtain DNA profiles using gel-based techniques. To explore whether cost-efficient techniques can produce results that are as robust as those obtained using high-throughput methods, we compared the performance of polyacrylamide gel electrophoresis (PAGE)- and capillary electrophoresis (CE)-derived genomic data in estimating genetic diversity and inferring relatedness using 70 individuals of fine flounder (Paralichthys adspersus) selected from a hatchery population and genotyped for five microsatellite loci.

RESULTS

Here, we show that PAGE- and CE-derived genomic datasets yield comparable genetic diversity levels regarding allelic diversity measures and heterozygosity. However, relatedness inferred from each dataset showed that the categorization of dyads in the different relationship categories strongly differed. This suggests that while scientists can reliably use PAGE-derived genomic data to estimate genetic diversity, they cannot use the same for parentage testing. The findings could help laboratories committed to population research not be discouraged from using the PAGE system if high-throughput technologies are unavailable and the method is adequate to address the biological question.

Perspectives on Individual Animal Identification from Biology and Computer Vision

Identifying individual animals is crucial for many biological investigations. In response to some of the limitations of current identification methods, new automated computer vision approaches have emerged with strong performance. Here, we review current advances of computer vision identification techniques to provide both computer scientists and biologists with an overview of the available tools and discuss their applications. We conclude by offering recommendations for starting an animal identification project, illustrate current limitations, and propose how they might be addressed in the future.

Long-term monitoring of a brown trout (Salmo trutta) population reveals kin-associated migration patterns and contributions by resident trout to the anadromous run

BACKGROUND

In species showing partial migration, as is the case for many salmonid fishes, it is important to assess how anthropogenic pressure experienced by migrating individuals affects the total population. We focused on brown trout (Salmo trutta) from the Guddal River in the Norwegian Hardanger Fjord system, which encompasses both resident and anadromous individuals. Aquaculture has led to increased anthropogenic pressure on brown trout during the marine phase in this region. Fish traps in the Guddal River allow for sampling all ascending anadromous spawners and descending smolts. We analyzed microsatellite DNA markers from all individuals ascending in 2006-2016, along with all emigrating smolts in 2017. We investigated (1) if there was evidence for declines in census numbers and effective population size during that period, (2) if there was association between kinship and migration timing in smolts and anadromous adults, and (3) to what extent resident trout were parents of outmigrating smolts.

RESULTS

Census counts of anadromous spawners showed no evidence for a decline from 2006 to 2016, but were lower than in 2000-2005. Estimates of effective population size also showed no trends of declines during the study period. Sibship reconstruction of the 2017 smolt run showed significant association between kinship and migration timing, and a similar association was indicated in anadromous spawners. Parentage assignment of 2017 smolts with ascending anadromous trout as candidate parents, and assuming that unknown parents represented resident trout, showed that 70% of smolts had at least one resident parent and 24% had two resident parents.

CONCLUSIONS

The results bear evidence of a population that after an initial decline has stabilized at a lower number of anadromous spawners. The significant association between kinship and migration timing in smolts suggests that specific episodes of elevated mortality in the sea could disproportionally affect some families and reduce overall effective population size. Finally, the results based on parentage assignment demonstrate a strong buffering effect of resident trout in case of elevated marine mortality affecting anadromous trout, but also highlight that increased mortality of anadromous trout, most of which are females, may lower overall production in the system.

Using Reciprocal Transplants to Assess Local Adaptation, Genetic Rescue, and Sexual Selection in Newly Established Populations

Small populations establishing on colonization fronts have to adapt to novel environments with limited genetic variation. The pace at which they can adapt, and the influence of genetic variation on their success, are key questions for understanding intraspecific diversity. To investigate these topics, we performed a reciprocal transplant experiment between two recently founded populations of brown trout in the sub-Antarctic Kerguelen Islands. Using individual tagging and genetic assignment methods, we tracked the fitness of local and foreign individuals, as well as the fitness of their offspring over two generations. In both populations, although not to the same extent, gene flow occurred between local and foreign gene pools. In both cases, however, we failed to detect obvious footprints of local adaptation (which should limit gene flow) and only weak support for genetic rescue (which should enhance gene flow). In the population where gene flow from foreign individuals was low, no clear differences were observed between the fitness of local, foreign, and F1 hybrid individuals. In the population where gene flow was high, foreign individuals were successful due to high mating success rather than high survival, and F1 hybrids had the same fitness as pure local offspring. These results suggest the importance of considering sexual selection, rather than just local adaptation and genetic rescue, when evaluating the determinants of success in small and recently founded populations.

Fast sequence-based microsatellite genotyping development workflow

Application of high-throughput sequencing technologies to microsatellite genotyping (SSRseq) has been shown to remove many of the limitations of electrophoresis-based methods and to refine inference of population genetic diversity and structure. We present here a streamlined SSRseq development workflow that includes microsatellite development, multiplexed marker amplification and sequencing, and automated bioinformatics data analysis. We illustrate its application to five groups of species across phyla (fungi, plant, insect and fish) with different levels of genomic resource availability. We found that relying on previously developed microsatellite assay is not optimal and leads to a resulting low number of reliable locus being genotyped. In contrast, de novo ad hoc primer designs gives highly multiplexed microsatellite assays that can be sequenced to produce high quality genotypes for 20-40 loci. We highlight critical upfront development factors to consider for effective SSRseq setup in a wide range of situations. Sequence analysis accounting for all linked polymorphisms along the sequence quickly generates a powerful multi-allelic haplotype-based genotypic dataset, calling to new theoretical and analytical frameworks to extract more information from multi-nucleotide polymorphism marker systems.

Parentage and relatedness reconstruction in Pinus sylvestris using genotyping-by-sequencing

Estimating kinship is fundamental for studies of evolution, conservation, and breeding. Genotyping-by-sequencing (GBS) and other restriction based genotyping methods have become widely applied in these applications in non-model organisms. However, sequencing errors, depth, and reproducibility between library preps could potentially hinder accurate genetic inferences. In this study, we tested different sets of parameters in data filtering, different reference populations and eight estimation methods to obtain a robust procedure for relatedness estimation in Scots pine (Pinus sylvestris L.). We used a seed orchard as our study system, where candidate parents are known and pedigree reconstruction can be compared with theoretical expectations. We found that relatedness estimates were lower than expected for all categories of kinship estimated if the proportion of shared SNPs was low. However, estimates reached expected values if loci showing an excess of heterozygotes were removed and genotyping error rates were considered. The genetic variance-covariance matrix (G-matrix) estimation, however, performed poorly in kinship estimation. The reduced relatedness estimates are likely due to false heterozygosity calls. We analyzed the mating structure in the seed orchard and identified a selfing rate of 3% (including crosses between clone mates) and external pollen contamination of 33.6%. Little genetic structure was observed in the sampled Scots pine natural populations, and the degree of inbreeding in the orchard seed crop is comparable to natural stands. We illustrate that under our optimized data processing procedure, relatedness, and genetic composition, including level of pollen contamination within a seed orchard crop, can be established consistently by different estimators.

Pedigree reconstruction from poor quality genotype data

Marker genotype data could suffer from a high rate of errors such as false alleles and allelic dropouts (null alleles) in situations such as SNPs from low-coverage next-generation sequencing and microsatellites from noninvasive samples. Use of such data without accounting for mistyping properly could lead to inaccurate or incorrect inferences of family relationships such as parentage and sibship. This study shows that markers with a high error rate are still informative. Simply discarding them could cause a substantial loss of precious information, and is impractical in situations where virtually all markers (e.g. SNPs from low-coverage next-generation sequencing, microsatellites from noninvasive samples) suffer from a similarly high error rate. This study also shows that some previous error models are valid for markers of low error rates, but fail for markers of high error rates. It proposes an improved error model and demonstrates, using simulated and empirical data of a high error rate (say, >0.5), that it leads to more accurate sibship and parentage inferences than previous models. It suggests that, in reality, markers of high error rates should be used rather than discarded in pedigree reconstruction, so long as the error rates can be estimated and used properly in the analyses.