Autobiologies on YouTube: narratives of direct-to-consumer genetic testing

Despite a growing personal genomics market, little is known about how people engage with the possibilities offered by direct-to-consumer (DTC) genetic testing. In order to help address this gap, this study deploys narrative analysis of YouTube videos posted by individuals who have purchased DTC genetic testing for disease. Genetic testing is said to be contributing to new states of illness, where individuals may become “patients-in-waiting.” In the videos analyzed, we found a new form of storytelling about this ambiguous state of illness, which we refer to as autobiology. Autobiology – the study of, and story about, one's own biology – concerns narratives of sense-making through forms of biological practice, as well as wayfaring narratives which interweave genetic markers and family histories of disease. These autobiologies – part of a broader shift toward public stories about genetics and other healthcare technologies – exhibit playfulness, as well as being bound with consumerist practices.     

Company disclosure and consumer perceptions of the privacy implications of direct-to-consumer genetic testing

This study examines the way direct-to-consumer genetic testing (DTCGT) companies communicate privacy information and how consumers understand privacy implications of DTCGT. We first conducted an analysis of DTCGT websites to determine what information they provide regarding the treatment of consumer information and samples. 86 companies offered DTCGT services that could be purchased online from Canada. We then surveyed 415 consumers (180 had purchased, 235 considered but did not purchase DTCGT). While most websites had some privacy information, few provided sufficient information for consumers to make informed purchase decisions. Nearly half of participants reported reading the company’s privacy policy and many felt they received enough information about privacy implications, but their expectations were generally not consistent with company practices. The most common expectation was that the company would share results only with them and destroy their sample after testing. We discuss these issues regarding privacy expectations in the context of DTCGT.     

Female mating preferences and offspring survival: testing hypotheses on the genetic basis of mate choice in a wild lekking bird

Indirect benefits of mate choice result from increased offspring genetic quality and may be important drivers of female behaviour. ‘Good‐genes‐for‐viability’ models predict that females prefer mates of high additive genetic value, such that offspring survival should correlate with male attractiveness. Mate choice may also vary with genetic diversity (e.g. heterozygosity) or compatibility (e.g. relatedness), where the female's genotype influences choice. The relative importance of these nonexclusive hypotheses remains unclear. Leks offer an excellent opportunity to test their predictions, because lekking males provide no material benefits and choice is relatively unconstrained by social limitations. Using 12 years of data on lekking lance‐tailed manakins, Chiroxiphia lanceolata, we tested whether offspring survival correlated with patterns of mate choice. Offspring recruitment weakly increased with father attractiveness (measured as reproductive success, RS), suggesting attractive males provide, if anything, only minor benefits via offspring viability. Both male RS and offspring survival until fledging increased with male heterozygosity. However, despite parent–offspring correlation in heterozygosity, offspring survival was unrelated to its own or maternal heterozygosity or to parental relatedness, suggesting survival was not enhanced by heterozygosity per se. Instead, offspring survival benefits may reflect inheritance of specific alleles or nongenetic effects. Although inbreeding depression in male RS should select for inbreeding avoidance, mates were not less related than expected under random mating. Although mate heterozygosity and relatedness were correlated, selection on mate choice for heterozygosity appeared stronger than that for relatedness and may be the primary mechanism maintaining genetic variation in this system despite directional sexual selection.     

Partitioning of genetic variation across the genome using multimarker methods in a wild bird population

The underlying basis of genetic variation in quantitative traits, in terms of the number of causal variants and the size of their effects, is largely unknown in natural populations. The expectation is that complex quantitative trait variation is attributable to many, possibly interacting, causal variants, whose effects may depend upon the sex, age and the environment in which they are expressed. A recently developed methodology in animal breeding derives a value of relatedness among individuals from high‐density genomic marker data, to estimate additive genetic variance within livestock populations. Here, we adapt and test the effectiveness of these methods to partition genetic variation for complex traits across genomic regions within ecological study populations where individuals have varying degrees of relatedness. We then apply this approach for the first time to a natural population and demonstrate that genetic variation in wing length in the great tit (Parus major) reflects contributions from multiple genomic regions. We show that a polygenic additive mode of gene action best describes the patterns observed, and we find no evidence of dosage compensation for the sex chromosome. Our results suggest that most of the genomic regions that influence wing length have the same effects in both sexes. We found a limited amount of genetic variance in males that is attributed to regions that have no effects in females, which could facilitate the sexual dimorphism observed for this trait. Although this exploratory work focuses on one complex trait, the methodology is generally applicable to any trait for any laboratory or wild population, paving the way for investigating sex‐, age‐ and environment‐specific genetic effects and thus the underlying genetic architecture of phenotype in biological study systems.     

Automated phylogenetic detection of recombination using a genetic algorithm

The evolution of homologous sequences affected by recombination or gene conversion cannot be adequately explained by a single phylogenetic tree. Many tree-based methods for sequence analysis, for example, those used for detecting sites evolving nonneutrally, have been shown to fail if such phylogenetic incongruity is ignored. However, it may be possible to propose several phylogenies that can correctly model the evolution of nonrecombinant fragments. We propose a model-based framework that uses a genetic algorithm to search a multiple-sequence alignment for putative recombination break points, quantifies the level of support for their locations, and identifies sequences or clades involved in putative recombination events. The software implementation can be run quickly and efficiently in a distributed computing environment, and various components of the methods can be chosen for computational expediency or statistical rigor. We evaluate the performance of the new method on simulated alignments and on an array of published benchmark data sets. Finally, we demonstrate that prescreening alignments with our method allows one to analyze recombinant sequences for positive selection.     

Substantial loss of genetic variation in a single generation of Senegalese sole (Solea senegalensis) culture: implications in the domestication process

The flatfish Solea senegalensis represents an important resource in modern mariculture and is largely raised in South Spain and Portugal. Substantial progress has been achieved in its domestication, though suitable reproduction and zootechnical conditions still remain unknown. Difficulties to obtain breeders from wild lead many companies to set up broodstocks with first generation (G1) progeny without genetic guidelines. To study the genetic processes underlying the early stage of domestication of this species, the genetic structure of four representative broodstocks from Southern Spain has been assessed by means of eight microsatellite loci . Data revealed a substantial reduction in levels of genetic variability on just one generation in stocks totally or partially composed of G1 individuals when compared with those solely integrated by individuals from wild. The genetic relatedness within the four stocks has been established, having detected close relationships between individuals from cultured origin, thus suggesting that the loss of variability is apparently due to setting up broodstocks by blind selecting of family related G1 individuals. The high proportion of siblings in these stocks can have negative consequences in future generations due to inbreeding effects. The relationships between the four broodstocks were traced, having found a common origin between two of them, which come from the same donor hatchery, thus enhancing the homogenization of the existent resources for S. senegalensis among the various stocks. This finding alerts about the risks in exchanging fish between hatcheries without knowing their genetic origin. From this study, the use of microsatellites is strongly recommended to control the genetic composition of S. senegalensis broodstocks, aimed to maintain standards of genetic health and improve their reproduction capacity, which is a key issue in the domestication process.     

重构司马光家族基因家谱

司马光家族延续了上千年,家谱记载较为完整,为谱牒学、历史学、遗传学等人文和自然学科的跨学科研究提供了较好的材料。本研究对11个声称为司马光后代的家族进行了Y-STR分型,结果表明有5个家族的STR单倍型彼此之间十分接近,同属下游单倍群O1a1a1a1a1a-F492+,F656-。因此,我们推断司马光家族的父系遗传类型极有可能属于此单倍群。同时,我们使用BATWING法逐层计算所有支系的最近共祖时间,其结果与根据谱牒资料构建的家族谱系图非常吻合。本项研究为从遗传学角度研究现代家族的父系谱系和重构家族谱牒材料提供了参考,并将有助于进一步研究汉代史学家司马迁家族以及西晋司马王室的源流。     

利用SPSS与AFLP方法对双丰甜菜品种（系）间亲缘关系与系谱分析比较

作物育种必须调查植物学性状和生物学特征指标数据,来建立种质资源库,利用SPSS多元分析方法克服了传统植物学性状和生物学特征指标难以综合评价的缺陷,探讨利用SPSS统计分析软件对双丰系列甜菜品种（系）间亲缘关系与系谱进行准确性分析,除双丰2号品种块根产量、产糖量和株高三个主成分具有极值影响外,结果基本与亲本分析一致,可以作为亲缘关系与系谱分析的一种辅助工具;通过AFLP获得不同基因型品种的特征带和特征缺失带,表明AFLP技术在甜菜品种鉴定上的应用潜力。但AFLP也具有缺点,主要是标记是共显性的,不能完全区分某一位点是杂合体和纯合体,因而不能更好地估算种群遗传的变异,对种群遗传结构的分析不能提供更多的统计信息,相信随着AFLP分子标记技术的不断完善与发展,将与SPSS统计分析软件一起越来越广泛地利用在种群遗传和系谱分析中。     

Colony genetic structure and queen mating frequency in fire ants of the subgenus Solenopsis (Hymenoptera: Formicidae)

Colony genetic structure was studied in natural populations of three fire ant taxa, Solenopsis richteri Forel, S. geminata (Fabr.), and hybrid S. invicta/richteri , using allozyme markers. All colonies studied exhibited arrays of female genotypes predicted under a model of monogyny (single functional queen) and monoandry (single insemination of queens). Males produced in the colonies appear to originate exclusively from the foundress queen, rather than from any virgin females present in the colonies. Thus these social insect colonies represent simple, albeit enormous, family groups. Single insemination and foundress parentage of males appear to be conserved reproductive traits in the subgenus Solenopsis , whereas another major determinant of colony genetic structure, the number of functional queens, is evolutionarily labile in this group.     

Estimation of genetic variability of the founder population in a conservation scheme using microsatellites

In a conservation programme with genealogical records it is possible to estimate the amount of variability of the founder population from a measure of the similarity among the individuals in the current population based on microsatellite markers. Here we compare three available methods and we shown that the one based on the molecular coancestry coefficient should be preferred.     

Close relatives in population samples: Evaluation of the consequences for genetic stock identification

Determining the origin of individuals in mixed population samples is key in many ecological, conservation and management contexts. Genetic data can be analyzed using genetic stock identification (GSI), where the origin of single individuals is determined using Individual Assignment (IA) and population proportions are estimated with Mixed Stock Analysis (MSA). In such analyses, allele frequencies in a reference baseline are required. Unknown individuals or mixture proportions are assigned to source populations based on the likelihood that their multilocus genotypes occur in a particular baseline sample. Representative sampling of populations included in a baseline is important when designing and performing GSI. Here, we investigate the effects of family sampling on GSI, using both simulated and empirical genotypes for Atlantic salmon (Salmo salar). We show that nonrepresentative sampling leading to inclusion of close relatives in a reference baseline may introduce bias in estimated proportions of contributing populations in a mixed sample, and increases the amount of incorrectly assigned individual fish. Simulated data further show that the induced bias increases with increasing family structure, but that it can be partly mitigated by increased baseline population sample sizes. Results from standard accuracy tests of GSI (using only a reference baseline and/or self‐assignment) gave a false and elevated indication of the baseline power and accuracy to identify stock proportions and individuals. These findings suggest that family structure in baseline population samples should be quantified and its consequences evaluated, before carrying out GSI.     

Evaluating the genetic status of a closed colony of titi monkeys (Callicebus cupreus) using multigenerational pedigrees

Pedigree metrics are essential for investigating colony genetic structure. The genetic structure of a closed Callicebus cupreus colony was examined using multigenerational pedigrees. Inbreeding was low, but genetic drift caused the loss of founder genome representation. Pedigrees can be used to detect founder representation and prevent bottlenecks and allele loss.     

Fitness effects of mutation: testing genetic redundancy in Arabidopsis thaliana

Screens of organisms with disruptive mutations in a single gene often fail to detect phenotypic consequences for the majority of mutants. One explanation for this phenomenon is that the presence of paralogous loci provides genetic redundancy. However, it is also possible that the assayed traits are affected by few loci, that effects could be subtle or that phenotypic effects are restricted to certain environments. We assayed a set of T‐DNA insertion mutant lines of Arabidopsis thaliana to determine the frequency with which mutation affected fitness‐related phenotypes. We found that between 8% and 42% of the assayed lines had altered fitness from the wild type. Furthermore, many of these lines exhibited fitness greater than the wild type. In a second experiment, we grew a subset of the lines in multiple environments and found whether a T‐DNA insert increased or decreased fitness traits depended on the assay environment. Overall, our evidence contradicts the hypothesis that genetic redundancy is a common phenomenon in A. thaliana for fitness traits. Evidence for redundancy from prior screens of knockout mutants may often be an artefact of the design of the phenotypic assays which have focused on less complex phenotypes than fitness and have used single environments. Finally, our study adds to evidence that beneficial mutations may represent a significant component of the mutational spectrum of A. thaliana.     

Colony genetic structure in the mono- and polygynous sibling species of the antsCamponotus nawai andCamponotus yamaokai: DNA fingerprint analysis

Using the ant-derived probe (pMY7), we performed DNA fingerprinting in monogynous and polygynous sibling ant speciesCamponotus nawai andCamponotus yamaokai. In monogynousC. nawai, band-sharing probabilities were low between unrelated individuals (mean 0.09), but those and relatedness estimates were consistently high between workers of the same nest (mean 0.85 and 0.74–0.83, respectively), suggesting that the queen mated once and nestmate workers are super-sisters. It also suggested monoandry: that is, that all nestmate workers shared most of the bands which were considered to have derived from a male. In polygynousC. yamaokai, band-sharing probabilities were low between queens of different populations (mean 0.13), moderate between queens of different nests in the same population (mean 0.25), but very high between queens of the same nest (within-nest means were 0.84–0.96). These results suggest that nestmate queens are genetically closely related with each other. Relatedness estimates between colony members sometimes reached 1. This might result from successive intranidal mating (inbreeding or large Wahlund effect) and adoption of new queens into the natal nests.     

Spatial genetic relationships in a population of the Japanese wood mouse Apodemus argenteus

Space-related relationships between individuals were investigated during the breeding season in a natural population of Apodemus argenteus (Temminck) by using the catch-mark-release method and microsatellite DNA markers. Several overlapping patterns of home ranges in breeding males and females were observed. Although this species is thought to be monogamous, DNA analysis revealed polygynous mating. In adults, relatedness between sexes was generally low and no apparent spatial genetic structure was observed. In juveniles, however, relatedness and geographical distance be-tween individuals were significantly negatively correlated. The relatedness between adult females decreased with distance, whereas there was not such a correlation in males. Long-distance movements were observed in current-year-born males. The differences in spatial genetic structure between adults and juveniles are thought to be produced by male-biased natal dispersal. An erratum to this article can be found at     

Strategies for genetic conservation of trees in the Peruvian Amazon

Forestry practices and high rates of land clearance for agriculture are causing genetic erosion of valuable tree species in the Peruvian Amazon, thereby endangering the economic sustainability of rural communities and limiting Peru's opportunities for the development of new timber and non-timber forest products. The potential utility and limitations of six low-input interventions to help forestall further genetic erosion in the region are discussed, with a focus on local community involvement. Improved agroforestry systems may help reduce deforestation by increasing farm productivity, although methods to increase the currently low adoption rate of these technologies need to be developed. Use of strategic tree domestication techniques can also improve farm productivity and prevent inadvertent genetic drift and inbreeding associated with traditional domestication practices, although to have a major impact, current programs need to be extended across the region. Woodlot forestry could supplant selective extraction of timber and offers an attractive opportunity for poverty alleviation if appropriate credit and land tenure policies can be developed. However, it may also result in increased deforestation if activities on public land cannot be controlled. The implementation of improved seed collection systems and simple seed transfer guidelines would help to reduce the collection of seed of poor quality and low genetic diversity, and avoid maladapted plantings, although such programs are difficult to monitor and seed costs may increase. Strategic identification and design of in situ conservation areas would help to ensure the viability of conserved populations, but requires the forfeiture of significant revenue from timber concessions.     

Extrapair fertilization and genetic similarity of social mates in the Mexican jay

Inbreeding depression should favor the ability of females toavoid inbreeding or minimize its effects. We tested for a relationshipbetween genetic similarity of social pairs and the occurrenceof extrapair fertilization (EPF) in the Mexican jay (Aphelocomaultramarina). Multilocus minisatellite and microsatellite DNAfingerprinting was used to detect extrapair young and measuregenetic similarity between social parents. We found that 12of 31 (39%) nests had at least one EPF and 15 of 93 (16%) youngwere the result of EPF. The mean DNA fingerprinting band sharingscore between social mates who had at least one EPF was significantlyhigher than the mean band sharing score between mates who didnot (0.35 versus 0.25). The mean band sharing score for non-EPFdyads (0.25) was similar to the background band sharing amongnonrelatives (0.23). The mean band sharing score for mates thathad an EPF was significantly higher than that of nonrelatives(background) and was significantly lower than that of half-siblings(0.52). Our results showed a highly significant relationshipbetween genetic similarity of social mates and incidence ofEPF.     

Characterizing the evolution of genetic variance using genetic covariance tensors

Determining how genetic variance changes under selection in natural populations has proved to be a very resilient problem in evolutionary genetics. In the same way that understanding the availability of genetic variance within populations requires the simultaneous consideration of genetic variance in sets of functionally related traits, determining how genetic variance changes under selection in natural populations will require ascertaining how genetic variance–covariance (G) matrices evolve. Here, we develop a geometric framework using higher-order tensors, which enables the empirical characterization of how G matrices have diverged among populations. We then show how divergence among populations in genetic covariance structure can then be associated with divergence in selection acting on those traits using key equations from evolutionary theory. Using estimates of G matrices of eight male sexually selected traits from nine geographical populations of Drosophila serrata, we show that much of the divergence in genetic variance occurred in a single trait combination, a conclusion that could not have been reached by examining variation among the individual elements of the nine G matrices. Divergence in G was primarily in the direction of the major axes of genetic variance within populations, suggesting that genetic drift may be a major cause of divergence in genetic variance among these populations.     

In the name of the migrant father--analysis of surname origins identifies genetic admixture events undetectable from genealogical records

Patrilineal heritable surnames are widely used to select autochthonous participants for studies on small-scale population genetic patterns owing to the unique link between the surname and a genetic marker, the Y-chromosome (Y-chr). Today, the question arises as to whether the surname origin will be informative on top of in-depth genealogical pedigrees. Admixture events that happened in the period after giving heritable surnames but before the start of genealogical records may be informative about the additional value of the surname origin. In this context, an interesting historical event is the demic migration from French-speaking regions in Northern France to the depopulated and Dutch-speaking region Flanders at the end of the sixteenth century. Y-chr subhaplogroups of individuals with a French/Roman surname that could be associated with this migration event were compared with those of a group with autochthonous Flemish surnames. Although these groups could not be differentiated based on in-depth genealogical data, they were significantly genetically different from each other. Moreover, the observed genetic divergence was related to the differences in the distributions of main Y-subhaplogroups between contemporary populations from Northern France and Flanders. Therefore, these results indicate that the surname origin can be an important feature on top of in-depth genealogical results to select autochthonous participants for a regional population genetic study based on Y-chromosomes.