Parentage analysis is a cornerstone of molecular ecology that has delivered fundamental insights into behaviour, ecology and evolution. Microsatellite markers have long been the king of parentage, ...their hypervariable nature conferring sufficient power to correctly assign offspring to parents. However, microsatellite markers have seen a sharp decline in use with the rise of next‐generation sequencing technologies, especially in the study of population genetics and local adaptation. The time is ripe to review the current state of parentage analysis and see how it stands to be affected by the emergence of next‐generation sequencing approaches. We find that single nucleotide polymorphisms (SNPs), the typical next‐generation sequencing marker, remain underutilized in parentage analysis but are gaining momentum, with 58 SNP‐based parentage analyses published thus far. Many of these papers, particularly the earlier ones, compare the power of SNPs and microsatellites in a parentage context. In virtually every case, SNPs are at least as powerful as microsatellite markers. As few as 100–500 SNPs are sufficient to resolve parentage completely in most situations. We also provide an overview of the analytical programs that are commonly used and compatible with SNP data. As the next‐generation parentage enterprise grows, a reliance on likelihood and Bayesian approaches, as opposed to strict exclusion, will become increasingly important. We discuss some of the caveats surrounding the use of next‐generation sequencing data for parentage analysis and conclude that the future is bright for this important realm of molecular ecology.
The effects of a phase-shifted photoperiod regime to advance maturation and spawning were examined in 3-year-old Pacific bluefin tuna Thunnus orientalis. Fish in three broodstock groups reared in sea ...cages were separately transferred at age 2 years to land-based indoor tanks, in June or July, in each of the three trial years; they were then exposed to a 2- or 2.5-month advanced photoperiod cycle. In all three trials, when the fish were 3 years old, the spawning was initiated 2–3 months before the normal spawning season. During the continuous spawning, the fish were maintained under a constant long photoperiod of 15 h light and water temperature of 24–25 °C. In the 2019/2020 trial, 114 spawning days were recorded between March and July 2020 in a group of 28–30 females and 23–28 males; in the 2020/2021 trial, 100 days were recorded between April and July 2021 in a group of 30–32 females and 20–22 males; and in the 2021/2022 trial, 138 days were recorded between April and September 2022 in a group of 6–8 females and 7–10 males. The number of eggs produced daily peaked 1–2 months after the onset of spawning and thereafter decreased. Egg diameter showed a negative relationship with days elapsed from the onset of spawning. The analysis of parentage assignment of the larvae in the 2019/2020 trial showed that at least 50% of females and 75% of males contributed to the spawning, whereas histological observation of gonads in the 2020/2021 trial showed that 33% of females completed vitellogenesis and 85% of males reached spermiation. The analysis of parentage assignment also showed that the spawning interval of females declined between March and June, and the mean number of eggs produced daily per female peaked in April and decreased until June. Our observations demonstrate that manipulation of a phase-shifted photoperiod regime is a powerful technique for advancing maturation and spawning in the Pacific bluefin tuna at age 3 years.
•A phase-shifted photoperiod advanced spawning of 3-year-old Pacific bluefin tuna.•Spawning was initiated in March or April and then recorded over 100 spawning events.•There was a negative relationship between egg size and days from onset of spawning.•The spawning interval of females declined between March and June.•The number of eggs produced daily per female peaked in April and decreased until June.
•It is possible to impute the genotype of a horse from those of its progeny.•Concordance rates increased as the number of genotyped progeny increased.•The inclusion of the dam’s genotype increased ...the concordance rates.•Allele concordance rate was always greater than the genotype concordance rate.•Genotype concordance rates ≥0.98 are achievable.
Many sport horse studbooks worldwide use microsatellite markers for parentage verification. However, many have expressed a desire to introduce genomic selection using genome-wide dense single nucleotide polymorphism (SNP) genotypes to complement their current breeding programs. Hence, it does not make sense to genotype the same animal for both microsatellite markers and SNPs markers. Transitioning to SNP-based parentage verification is an obvious solution but one barrier to this transition is the lack of SNP data on parents from which to verify parentage against. Therefore, the objective of this study was to assess the ability to impute the SNP genotype of a stallion from the genotypes of its progeny, with or without the consideration of the genotype of the progeny’s dam. Genotype information from 55 935 SNPs was available on 13 327 horses. A total of 98 stallions had genotype data on 10 progeny and the genotypes of these stallions were used as a test population. Genome-wide genotype imputation was undertaken combining a family- and population-based imputation approach. Several different scenarios were assessed to quantify the ability to accurately impute the genotype of a stallion based on genotype data of incrementally more half-sibling progeny. Using genomic information from four progeny the average genotype concordance of the imputed sire genotype compared to the actual sire’s genotype was 0.932. The average genotype concordance rate increased to 0.960 when the genotypes of 10 progeny were included in the imputation process. The inclusion of the genotypes of the dams of the progeny improved the concordance rate from 0.932 to 0.977 when based on the genotype of just four progeny and their dams and from 0.960 to 0.996 when based on the genotype of 10 progeny and their dams. These results suggest it is possible to impute the genotype of a non-genotyped horse from the genotypes of its progeny and that the inclusion of the genotypes of the dams of the progeny improves this imputation accuracy further.
Postpartum depression and low parental self‐efficacy (PSE) are risk factors for poor child behavior. Little is known, however, about the course of dual trajectories of cooccurring depressive symptoms ...and PSE or its impact on children's socioemotional development. This study sought to identify trajectories of postpartum PSE and depressive symptoms in new, first‐time mothers using growth mixture modeling. Results demonstrated a class of women with “low risk” (88.8%) who manifested low levels of depression and high levels of PSE during the postpartum period; a second group of women, labeled “early risk” (6.3%) with high levels of depression that decreased over time but lower levels of PSE that remained fairly stable; and a final trajectory group deemed the “late‐risk” class (4.9%) with initially low levels of depression and high levels of PSE that significantly increased and decreased, respectively, over the period. Early childhood trauma, parenting stress, and poor parenting practices were associated membership in a high‐risk class. Mothers in the high‐risk groups reported children with more aggressive and defiant behavior at age 3. We conclude by discussing the implications of our findings for developing effective and sensitive interventions.
Resumen
La depresión posterior al parto y la autoeficacia de los padres (PSE) son factores de riesgo para la débil conducta del niño. Poco se sabe, sin embargo, acerca del curso de las trayectorias duales de síntomas depresivos que ocurren simultáneamente y PSE o su impacto en el desarrollo socioemocional de los niños. Este estudio se propuso identificar las trayectorias del PSE posterior al parto y los síntomas depresivos en nuevas, primerizas mamás usando un modelo de mezcla de crecimiento. Los resultados mostraron una clase de mujeres con ‘bajo riesgo’ (88.8%) que manifestaron bajos niveles de depresión y altos niveles de PSE durante el período posterior al parto; un segundo grupo de mujeres, llamado ‘de temprano riesgo’ (6.3%) con altos niveles de depresión que disminuyeron a lo largo del tiempo, pero más bajos niveles de PSE que se mantuvieron equitativamente estables; y un final grupo de trayectoria denominado la clase del ‘riesgo tardío’ (4.9%) con iniciales bajos niveles de depresión y altos niveles de PSE que significativamente aumentaron y disminuyeron, respectivamente, a lo largo del período. El trauma en la temprana niñez, el estés de crianza, así como las débiles prácticas de crianza fueron afiliaciones asociadas dentro de una clase de alto riesgo. Las mamás en los grupos de alto riesgo reportaron niños con conductas más agresivas y desafiantes a la edad de tres años. Concluimos con una discusión de las implicaciones de nuestros resultados para desarrollar intervenciones eficaces y sensibles.
Résumé
La dépression postpartum et l'auto‐efficacité parentale (abrégé en français ici AEP) sont des facteurs de risque pour les problèmes de comportement de l'enfant. On sait peu de choses, cependant, à propos du cours des trajectoires duels des symptômes dépressifs concomitants et l'AEP ou son impact sur le développement socio‐émotionnel des enfants. Cette étude a cherché à identifier les trajectoires d'AEP postpartum et de symptômes dépressifs chez des mères étant mères pour la première fois, en utilisant un modèle de croissance mixte. Les résultats ont fait état d'une classe de femmes avec un “risque moindre” (88,8%) qui faisaient preuve de niveaux peu élevés de dépression et de niveaux élevés d'AEP durant la période postpartum; un deuxième groupe de femmes, appelé “risque précoce” (6,3%) avec des niveaux élevés de dépression qui ont décru au fil du temps et avec des niveaux plus bas d'AEP qui restaient relativement stables; et un groupe de trajectoire finale estimé comme étant la classe de ‘risque tardif’ (4,9%) avec initialement des niveaux moindres de dépression et des niveaux élevés d'AEP qui ont respectivement augmenté et baissé de manière importante, au fil de cette période. Le trauma de la petite enfance, le stress de parentage et de mauvaises pratiques parentales étaient liés à l'appartenance à la classe à haut risque. Les mères des groupes à risque élevé ont fait état d'enfants avec un comportement plus agressif et défiant à l’âge de trois ans. Nous concluons en discutant les implications pour le développement d'interventions efficaces et sensibles.
Zusammenfassung
Duale Verläufe elterlicher Selbstwirksamkeit sowie depressiver Symptomatik bei postpartalen Müttern und deren Auswirkungen auf die sozio‐emotionale Anpassung im frühen Kindesalter: Ein Growth Mixture Modell
Postpartale Depression und elterliche Selbstwirksamkeit (parental self‐efficacy; PSE) sind Risikofaktoren für nachteiliges kindliches Verhalten. Es ist jedoch wenig bekannt über den Verlauf gemeinsam auftretender depressiver Symptomatik und PSE oder deren Auswirkung auf die sozio‐emotionale Entwicklung der Kinder. In dieser Studie wurde versucht, mit Hilfe von Growth Mixture Modellierung Verläufe von postpartaler PSE und depressiver Symptomatik bei Erstgebärenden zu identifizieren. Die Ergebnisse zeigten drei Gruppen auf. Die erste Gruppe bestand aus Frauen mit “niedrigem Risiko” (88,8%), die während der postpartalen Phase niedrige Depressions‐ und hohe PSE‐Werte hatten. Die zweite Gruppe bestand aus Frauen mit “frühem Risiko” (6,3%), die anfänglich hohe aber im Laufe der Zeit abnehmende Depressionswerte und niedrigere, ziemlich stabil bleibenden PSE‐Werte hatten. Die letzte Verlaufs‐Gruppe bestand aus Frauen mit “spätem Risiko” (4,9%), die anfänglich niedrige Depressions‐ und hohe PSE‐Werte hatten, die im Laufe der Zeit signifikant anstiegen bzw. abnahmen. Frühkindliches Trauma, elterlicher Stress und nachteilige Erziehungspraktiken waren mit der Zugehörigkeit zu einer Hochrisikoklasse assoziiert. Mütter in den Hochrisikogruppen berichteten von Kindern mit mehr aggressivem und trotzigem Verhalten im Alter von drei Jahren. Abschließend werden die Implikationen unserer Ergebnisse für die Entwicklung effektiver und sensibler Interventionen diskutiert.
抄録
第一子産後の母親における育児自己効力感及び抑うつ症状と早期幼児期の社会情緒的適応の2つの軌跡:成長混合モデル
産後うつと育児自己効力感 (PSE) は子どもの問題行動を引き起こす危険因子である。しかし、併発する抑うつ症状と自己効力感あるいはその影響による子どもの社会情緒の発達がたどる2つの軌跡についてはほとんど知られていない。この研究は成長混合モデリングを用いて、第一子産後の母親に生じる育児自己効力感と抑うつ症状の軌跡を同定しようとするものである。結果は以下のようであった。‘低リスク’の女性グループ (88.8％) は、産後の抑うつレベルが低く、育児自己効力感が高かった。第二グループ (6.3％) の女性は‘早期リスク’とされ、抑うつレベルが高くても時間経過で治まるものだが、育児自己効力感は低くその後も変わらない。最後の軌跡のグループ (4.9％) は‘後期リスク’と見なされるが、はじめ抑うつレベルは低く育児自己効力感は高いのだが、時を経る中でそれぞれ大幅に上がり、そして下がる。早期幼児期のトラウマ、育児ストレス、そして未熟な育児実践が、高リスクに伴って見られた。高リスクグループの母親は3歳時の子どもが攻撃的で反抗的だったと報告した。私達は、この研究結果の意味を検討して効果的で慎重な介入を開発することとする。
摘要
产后抑郁症和父母自我效能感 (PSE) 是儿童不良行为的危险因素。然而, 关于抑郁症状和PSE同时发生的双轨迹过程及其对儿童社交情感发展的影响知之甚少。本研究试图通过生长混合模型来确定初产母亲产后PSE和抑郁症状的发展轨迹。结果显示, 第一组“低风险”女性 (88.8%) 在产后表现出低水平的抑郁和高水平的PSE;第二组女性, 被标记为“早期风险” (6.3%) , 其抑郁程度会随着时间的推移而降低, 但PSE水平较低并保持相当稳定;最后一个轨迹组认为是“晚期风险”类别 (4.9%) , 其最初具有低水平的抑郁和高水平的PSE, 但在这段时间内分别显著增加和减少。儿童早期创伤、育儿压力和不良的育儿习惯与高风险类别的组员身份有关。高危组的母亲报告说, 孩子在三岁时表现出更具攻击性和挑衅性的行为。最后, 我们讨论了研究结果对制定有效和敏感的干预措施的影响。
ملخص
المسارات المزدوجة للفعالية الذاتية للتربية الوالدية وأعراض الاكتئاب عند الأمهات الجديدات بعد الولادة والتكيف الاجتماعي العاطفي في مرحلة الطفولة المبكرة: نموذج خليط النمو
الاكتئاب بعد الولادة والفعالية الذاتية للوالدين(PSE) هي عوامل خطر لسوء سلوك الطفل. ومع ذلك، لا يعرف الكثير عن تطور المسار المزدوج لأعراض الاكتئاب المتزامنة والكفاءة الذاتية للتربية الوالدية أو تأثيرها على النمو الاجتماعي العاطفي للأطفال. سعت هذه الدراسة إلى تحديد مساراتPSE بعد الولادة وأعراض الاكتئاب عند الأمهات الجدد لأول مرة باستخدام نمذجة خليط النمو . وأظهرت النتائج وجود فئة من النساء ذوات “المخاطر المنخفضة” (88.8 في المائة) من النساء اللاتي أظهرن مستويات منخفضة من الاكتئاب ومستويات عالية من PSE خلال فترة ما بعد الولادة؛ ومجموعة ثانية من النساء، وصفت ب “الخطر المبكر” (6.3٪) مع مستويات عالية من الاكتئاب انخفضت مع مرور الوقت ومستويات منخفضة من PSE والتي ظلت مستقرة إلى حد ما. كما وجدت مجموعة أخيرة وصفت بمجموعة “المخاطر المتأخرة” (4.9٪) مع مستويات منخفضة في البداية من الاكتئاب وارتفاع مستويات PSE والتي زادت وانخفضت بشكل ملحوظ ، على التوالي، على مدى فترة الدراسة. وارتبطت صدمة الطفولة المبكرة، والإجهاد الأبوي، وسوء ممارسات التربية بالانتماء إلى أحد هذه المجموعات ذات المخاطرة العالية. وأبلغت الأمهات في فئات المخاطرة العالية عن أطفال يعانون من سلوك أكثر عدوانية وعناداً في سن الثالثة. وتختم الدراسة بمناقشة تطبيقات النتائج لتطوير تدخلات فعالة وحساسة.
Networks of no-take marine protected areas (MPAs) have been widely advocated for the conservation of marine biodiversity. But for MPA networks to be successful in protecting marine populations, ...individual MPAs must be self-sustaining or adequately connected to other MPAs via dispersal. For marine species with a dispersive larval stage, populations within MPAs require either the return of settlement-stage larvae to their natal reserve or connectivity among reserves at the spatial scales at which MPA networks are implemented. To date, larvae have not been tracked when dispersing from one MPA to another, and the relative magnitude of local retention and connectivity among MPAs remains unknown. Here we use DNA parentage analysis to provide the first direct estimates of connectivity of a marine fish, the orange clownfish (Amphiprion percula), in a proposed network of marine reserves in Kimbe Bay, Papua New Guinea. Approximately 40% of A. percula larvae settling into anemones in an island MPA at 2 different times were derived from parents resident in the reserve. We also located juveniles spawned by Kimbe Island residents that had dispersed as far as 35 km to other proposed MPAs, the longest distance that marine larvae have been directly tracked. These dispersers accounted for up to 10% of the recruitment in the adjacent MPAs. Our findings suggest that MPA networks can function to sustain resident populations both by local replenishment and through larval dispersal from other reserves. More generally, DNA parentage analysis provides a direct method for measuring larval dispersal for other marine organisms.
A major use of genetic data is parentage verification and identification as inaccurate pedigrees negatively affect genetic gain. Since 2012 the international standard for single nucleotide ...polymorphism (SNP) verification in
cattle has been the ISAG SNP panels. While these ISAG panels provide an increased level of parentage accuracy over microsatellite markers (MS), they can validate the wrong parent at ≤1% misconcordance rate levels, indicating that more SNP are needed if a more accurate pedigree is required. With rapidly increasing numbers of cattle being genotyped in Ireland that represent 61
breeds from a wide range of farm types: beef/dairy, AI/pedigree/commercial, purebred/crossbred, and large to small herd size the Irish Cattle Breeding Federation (ICBF) analyzed different SNP densities to determine that at a minimum ≥500 SNP are needed to consistently predict only one set of parents at a ≤1% misconcordance rate. For parentage validation and prediction ICBF uses 800 SNP (ICBF800) selected based on SNP clustering quality, ISAG200 inclusion, call rate (CR), and minor allele frequency (MAF) in the Irish cattle population. Large datasets require sample and SNP quality control (QC). Most publications only deal with SNP QC via CR, MAF, parent-progeny conflicts, and Hardy-Weinberg deviation, but not sample QC. We report here parentage, SNP QC, and a genomic sample QC pipelines to deal with the unique challenges of >1 million genotypes from a national herd such as SNP genotype errors from mis-tagging of animals, lab errors, farm errors, and multiple other issues that can arise. We divide the pipeline into two parts: a Genotype QC and an Animal QC pipeline. The Genotype QC identifies samples with low call rate, missing or mixed genotype classes (no BB genotype or ABTG alleles present), and low genotype frequencies. The Animal QC handles situations where the genotype might not belong to the listed individual by identifying: >1 non-matching genotypes per animal, SNP duplicates, sex and breed prediction mismatches, parentage and progeny validation results, and other situations. The Animal QC pipeline make use of ICBF800 SNP set where appropriate to identify errors in a computationally efficient yet still highly accurate method.
Fueled by direct-to-consumer (DTC) genetic testing and genetic-relative finder services, some participants in genetic 8genealogy databases are making “not parent expected” (NPE) discoveries. To ...better understand experiences of this phenomenon, we surveyed a large cohort of users of genetic relative finder (GRF) services concerning their experiences after an NPE discovery.
Using thematic analysis, we analyzed responses from a cohort of GRF users (n = 646) to open-ended survey items to understand these experiences and their recommendations for DTC genetic testing companies and other GRF users.
We found that individuals had both positive and negative emotional experiences related to the NPE discovery. Positive aspects included deeper self-understanding, connecting with new family members, and uncovering answers to questions. Negative aspects included rejection by new genetic relatives, inability to seek answers from relatives who had already died, and impairment of family relationships, especially with mothers. For many participants, the challenges after the discovery nevertheless felt worthwhile because the truth was uncovered. Perhaps notably, some participants suggested enhanced warnings prediscovery and improved support after discovery from companies who provide DTC genetic testing services.
GRF services are powerful tools for family research and genealogy. Despite some possible positive and worthwhile experiences arising from making an NPE discovery, GRF users risk dealing with this potentially life-altering experience without adequate support. Participants in this study recommended an increase in resources from DTC genetic testing companies that could help users anticipate and navigate an NPE discovery.
Extra‐pair paternity in birds Brouwer, Lyanne; Griffith, Simon C.
Molecular ecology,
November 2019, Volume:
28, Issue:
22
Journal Article
Peer reviewed
Open access
Since the first molecular study providing evidence for mating outside the pair bond in birds over 30 years ago, >500 studies have reported rates of extra‐pair paternity (EPP) in >300 bird species. ...Here, we give a detailed overview of the current literature reporting EPP in birds and highlight the sampling biases and patterns in the data set with respect to taxonomy, avian phylogeny and global regions, knowledge of which will be crucial for correct interpretation of results in future comparative studies. Subsequently, we use this comprehensive dataset to simultaneously test the role of several ecological and life history variables. We do not find clear evidence that variation in EPP across socially monogamous species can be explained by latitude, density (coloniality), migration, generation length, genetic structuring (dispersal distance), or climatic variability, after accounting for phylogeny. These results contrast previous studies, most likely due to the large heterogeneity within species in both EPP and the predictor of interest, indicating that using species averages might be unreliable. Despite the absence of broadscale ecological drivers in explaining interspecific variation in EPP, we suggest that certain behaviours and ecological variables might facilitate or constrain EPP, as indicated by our finding that EPP was negatively associated with latitude within noncolonial species, suggesting a role of breeding synchrony. Thus, rather than focussing on general explanations for variation in EPP across all species, a future focus should be on how various aspects of ecology or life history might have driven variation in EPP among groups of species or populations of the same species. Hence, we argue that variation in EPP can be partly explained when taking the right perspective. This comprehensive overview, and particularly the dataset provided herein will create a foundation for further studies.
Research framework : The aspiration of sexual minorities to gain access to a kinship from which they were once excluded, the decline in the average age of first pregnancies and the multifactorial ...phenomenon of a decreasing number of adoptable children all point to the need to think differently about adoption, accepting that it needs not be exclusive of maintaining ties with the parents of origin. Objectives : The aim of this paper is to identify what adjustments could be made to enable simple adoption to realize its full potential in contemporary society.Methodology: The study was based primarily on an analysis of French legislation and jurisprudence, as well as theoretical insights, while also making allowance for comparative law (Canada, the United States and Cuba). Results: It appears that, despite the obvious need for greater recognition of elective filiation in a context of disconnection between biology and kinship, the idea of recognizing genuine pluriparentage remains difficult for the French legislature to accept, and that simple adoption remains devalued as a secondary source of filiation. Conclusions : To unleash the potential of simple adoption, it would suffice to make a few simple adjustments: equivalence of rights in terms of parental authority or inheritance taxation, use in the context of child protection and extension to all situations of multiple kinship, where it is in the child’s interest to have an additive parent recognized. Contribution : This article shows that the persistent difficulty of the French legislator to draw the consequences of recent societal evolutions, that it has nevertheless accompanied, is essentially linked to the tenacity of the myth of begetting, and that major evolutions could be achieved without much effort, for the benefit of children.
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