The pink pigeon (Nesoenas mayeri) is an endemic species of Mauritius that has made a remarkable recovery after a severe population bottleneck in the 1970s to early 1990s. Prior to this bottleneck, an ...ex situ population was established from which captive‐bred individuals were released into free‐living subpopulations to increase population size and genetic variation. This conservation rescue led to rapid population recovery to 400–480 individuals, and the species was twice downlisted on the International Union for the Conservation of Nature (IUCN) Red List. We analyzed the impacts of the bottleneck and genetic rescue on neutral genetic variation during and after population recovery (1993–2008) with restriction site‐associated sequencing, microsatellite analyses, and quantitative genetic analysis of studbook data of 1112 birds from zoos in Europe and the United States. We used computer simulations to study the predicted changes in genetic variation and population viability from the past into the future. Genetic variation declined rapidly, despite the population rebound, and the effective population size was approximately an order of magnitude smaller than census size. The species carried a high genetic load of circa 15 lethal equivalents for longevity. Our computer simulations predicted continued inbreeding will likely result in increased expression of deleterious mutations (i.e., a high realized load) and severe inbreeding depression. Without continued conservation actions, it is likely that the pink pigeon will go extinct in the wild within 100 years. Conservation rescue of the pink pigeon has been instrumental in the recovery of the free‐living population. However, further genetic rescue with captive‐bred birds from zoos is required to recover lost variation, reduce expression of harmful deleterious variation, and prevent extinction. The use of genomics and modeling data can inform IUCN assessments of the viability and extinction risk of species, and it helps in assessments of the conservation dependency of populations.
Resumen
La paloma rosada (Nesoenas mayeri) es una especie endémica de Mauricio que se ha recuperado impresionantemente después de un grave cuello de botella poblacional a principios de la década de 1970 que duró hasta inicios de la década de 1990. Antes de este cuello de botella se había establecido una población ex situ de la cual se liberaban individuos reproducidos en cautiverio a las subpoblaciones en libertad para incrementar la variación genética y el tamaño poblacional. Este rescate de conservación derivó en una recuperación rápida de la población (400‐480 individuos) y la especie cambió positivamente de categoría dos veces en la Lista Roja de la Unión Internacional para la Conservación de la Naturaleza (UICN). Analizamos los impactos del cuello de botella y el rescate genético sobre la variación genética neutral durante y después de la recuperación poblacional (de 1993 a 2008) mediante secuenciación RAD, análisis de microsatélites y análisis genéticos cuantitativos de los datos del libro genealógico de 1112 aves ubicadas en zoológicos de Europa y los Estados Unidos. Usamos simulaciones por computadora para estudiar los cambios pronosticados en la variación genética y en la viabilidad poblacional del pasado hacia el futuro. La variación genética declinó rápidamente, a pesar de la recuperación poblacional, y el tamaño efectivo de la población fue aproximadamente un orden de magnitud más pequeño que el tamaño del censo. La especie contó con una carga genética elevada de casi 15 equivalentes letales para la longevidad. Nuestras simulaciones pronostican que la endogamia continua probablemente resultará en un incremento en la expresión de mutaciones deletéreas (es decir, una carga realizada elevada) y en una depresión endogámica severa. Sin acciones continuas para la conservación, es probable que la paloma rosada esté extinta en vida libre dentro de cien años. El rescate de conservación de la paloma rosada ha sido fundamental en la recuperación de la población silvestre; sin embargo, se requiere de un rescate genético adicional con las aves de reproducción en cautiverio de los zoológicos para recuperar la variación perdida, reducir la expresión de la variación deletérea dañina y prevenir la extinción. El uso de la genómica y los datos modelados puede orientar las valoraciones de la UICN sobre la viabilidad y el riesgo de extinción de las especies, además de que ayuda en la evaluación de la dependencia que tienen las poblaciones de la conservación.
Avoiding extinction in a rapidly changing environment often relies on a species’ ability to quickly adapt in the face of extreme selective pressures. In Panamá, two closely related harlequin frog ...species (Atelopus varius and Atelopus zeteki) are threatened with extinction due to the fungal pathogen Batrachochytrium dendrobatidis (Bd). Once thought to be nearly extirpated from Panamá, A. varius have recently been rediscovered in multiple localities across their historical range; however, A. zeteki are possibly extinct in the wild. By leveraging a unique collection of 186 Atelopus tissue samples collected before and after the Bd outbreak in Panama, we describe the genetics of persistence for these species on the brink of extinction. We sequenced the transcriptome and developed an exome‐capture assay to sequence the coding regions of the Atelopus genome. Using these genetic data, we evaluate the population genetic structure of historical A. varius and A. zeteki populations, describe changes in genetic diversity over time, assess the relationship between contemporary and historical individuals, and test the hypothesis that some A. varius populations have rapidly evolved to resist or tolerate Bd infection. We found a significant decrease in genetic diversity in contemporary (compared to historical) A. varius populations. We did not find strong evidence of directional allele frequency change or selection for Bd resistance genes, but we uncovered a set of candidate genes that warrant further study. Additionally, we found preliminary evidence of recent migration and gene flow in one of the largest persisting A. varius populations in Panamá, suggesting the potential for genetic rescue in this system. Finally, we propose that previous conservation units should be modified, as clear genetic breaks do not exist beyond the local population level. Our data lay the groundwork for genetically informed conservation and advance our understanding of how imperiled species might be rescued from extinction.
In Panamá, two closely related harlequin frog species (Atelopus varius, Atelopus zeteki) are threatened with extinction due to Batrachochytrium dendrobatidis (Bd). We sequenced 186 Atelopus tissues collected before and after the Bd outbreak in Panamá using a custom exome capture assay and found an overall decrease in genetic diversity. We uncovered a set of disease‐related candidate genes that warrant further study and found preliminary evidence of admixture in the largest contemporary A. varius population, suggesting the potential for genetic rescue. We propose that previous conservation units should be modified, as clear genetic breaks do not exist beyond the population level.
Genetic rescue is an increasingly considered conservation measure to address genetic erosion associated with habitat loss and fragmentation. The resulting gene flow from facilitating migration may ...improve fitness and adaptive potential, but is not without risks (e.g., outbreeding depression). Here, we conducted a test of genetic rescue by translocating ten (five of each sex) brook trout (Salvelinus fontinalis) from a single source to four nearby and isolated stream populations. To control for the demographic contribution of translocated individuals, ten resident individuals (five of each sex) were removed from each recipient population. Prior to the introduction of translocated individuals, the two smallest above‐barrier populations had substantially lower genetic diversity, and all populations had reduced effective number of breeders relative to adjacent below‐barrier populations. In the first reproductive bout following translocation, 31 of 40 (78%) translocated individuals reproduced successfully. Translocated individuals contributed to more families than expected under random mating and generally produced larger full‐sibling families. We observed relatively high (>20%) introgression in three of the four recipient populations. The translocations increased genetic diversity of recipient populations by 45% in allelic richness and 25% in expected heterozygosity. Additionally, strong evidence of hybrid vigour was observed through significantly larger body sizes of hybrid offspring relative to resident offspring in all recipient populations. Continued monitoring of these populations will test for negative fitness effects beyond the first generation. However, these results provide much‐needed experimental data to inform the potential effectiveness of genetic rescue‐motivated translocations.
Evaluating the outcomes of genetic rescue attempts Robinson, Zachary L.; Bell, Donovan A.; Dhendup, Tashi ...
Conservation biology,
April 2021, 2021-04-00, 20210401, Volume:
35, Issue:
2
Journal Article
Peer reviewed
Augmenting gene flow is a powerful tool for the conservation of small, isolated populations. However, genetic rescue attempts have largely been limited to populations at the brink of extinction, in ...part due to concerns over negative outcomes (e.g., outbreeding depression). Increasing habitat fragmentation may necessitate more proactive genetic management. Broader application of augmented gene flow will, in turn, require rigorous evaluation to increase confidence and identify pitfalls in this approach. To date, there has been no assessment of best monitoring practices for genetic rescue attempts. We used genomically explicit, individual‐based simulations to examine the effectiveness of common approaches (i.e., tests for increases in fitness, migrant ancestry, heterozygosity, and abundance) for determining whether genetic rescue or outbreeding depression occurred. Statistical power to detect the effects of gene flow on fitness was high (≥0.8) when effect sizes were large, a finding consistent with those from previous studies on severely inbred populations. However, smaller effects of gene flow on fitness can appreciably affect persistence probability but current evaluation approaches fail to provide results from which reliable inferences can be drawn. The power of the metrics we examined to evaluate genetic rescue attempts depended on the time since gene flow and whether gene flow was beneficial or deleterious. Encouragingly, the use of multiple metrics provided nonredundant information and improved inference reliability, highlighting the importance of intensive monitoring efforts. Further development of best practices for evaluating genetic rescue attempts will be crucial for a responsible transition to increased use of translocations to decrease extinction risk.
Evaluación de los Resultados de los Intentos de Rescate Genético
Resumen
El aumento del flujo génico es una herramienta poderosa para la conservación de poblaciones pequeñas y aisladas. Sin embargo, los intentos de rescate genético en su mayoría se han limitado a las poblaciones que se encuentran al borde de la extinción, en parte debido a la preocupación que existe por los resultados negativos (es decir, la depresión exogámica). La creciente fragmentación del hábitat puede requerir un manejo genético más proactivo. La aplicación más extensa del flujo génico aumentado requerirá a su vez una evaluación rigurosa para incrementar la confianza e identificar las dificultades de esta estrategia. A la fecha, no ha habido una evaluación de las mejores prácticas de monitoreo para los intentos de rescate genético. Usamos simulaciones explícitas basadas en individuos para examinar la efectividad de las estrategias comunes (es decir, análisis del incremento en adaptabilidad, ascendencia migratoria, heterocigosidad y abundancia) para determinar si ocurrió el rescate genético o la depresión exogámica. El poder estadístico para detectar los efectos del flujo génico sobre la adaptabilidad fue elevado (≥0.8) cuando el tamaño de los efectos fue grande, un hallazgo consistente con aquellos realizados en estudios previos sobre poblaciones con una endogamia severa. Sin embargo, los efectos menores del flujo génico sobre la adaptabilidad pueden afectar de manera apreciable la probabilidad de persistencia, pero las estrategias actuales de evaluación no proporcionan resultados de los cuales se puedan hacer inferencias confiables. El poder de las medidas que examinamos para evaluar los intentos de rescate genético dependió del tiempo desde que inició el flujo génico y de si el flujo génico fue benéfico o perjudicial. De manera alentadora, el uso de múltiples medidas proporcionó información no redundante y mejoró la confiabilidad de la inferencia, resaltando así la importancia de los esfuerzos intensivos de monitoreo. El futuro desarrollo de mejores prácticas para la evaluación de los intentos de rescate genético será de suma importancia para la transición responsable hacia el mayor uso de reubicaciones para reducir el riesgo de extinción.
摘要
扩大基因流是保护孤立小种群的有力工具。然而, 遗传拯救的尝试很大程度上局限于濒临灭绝的种群, 部分原因是担忧出现负面结果 (如远交衰退) 。目前, 栖息地的日益破碎化正在迫使人们采取更积极的遗传管理措施。增加基因流的广泛应用也需要严格的评估, 以增强对这种方法的信心并识别其中的缺陷。迄今为止, 还没有研究对遗传拯救尝试的最佳监测实践进行评估。本研究使用基于个体的基因组显式模拟检验了常见方法的有效性(检验适合度是否增加、迁徙遗传祖先、杂合度和丰度), 以确定是否实现了遗传拯救或发生了远交衰退。当效应量较大时, 检测基因流对适合度影响的统计功效很高 (≥0.8), 这一发现与之前对严重近交群体的研究结果一致。然而, 基因流对适合度较小的影响也可以显著影响种群续存的概率, 但目前的评估方法无法提供能够得出可靠推论的结果。我们用来评估遗传拯救尝试的指标的功效取决于基因流发生的时间以及基因流产生了有益还是有害的影响。令人鼓舞的是, 使用多重指标可以提供非冗余信息并提高推断的可靠性, 这突出了加强监控工作的重要性。进一步发展评估遗传拯救尝试的最佳方法, 对于负责任地逐步增加迁地保护的使用以减少灭绝风险将是至关重要的。【翻译: 胡怡思; 审校: 聂永刚】
Article impact statement: Commonly used monitoring approaches frequently fail to detect the substantial conservation benefits of augmented gene flow.
Abstract
In the mid-1990s, the population size of Florida panthers became so small that many individuals manifested traits associated with inbreeding depression (e.g., heart defects, cryptorchidism, ...high pathogen-parasite load). To mitigate these effects, pumas from Texas were introduced into South Florida to augment genetic variation in Florida panthers. In this study, we report a de novo puma genome assembly and annotation after resequencing 10 individual genomes from partial Florida-Texas-F1 trios. The final genome assembly consisted of ∼2.6 Gb and 20,561 functionally annotated protein-coding genes. Foremost, expanded gene families were associated with neuronal and embryological development, whereas contracted gene families were associated with olfactory receptors. Despite the latter, we characterized 17 positively selected genes related to the refinement of multiple sensory perceptions, most notably to visual capabilities. Furthermore, genes under positive selection were enriched for the targeting of proteins to the endoplasmic reticulum, degradation of mRNAs, and transcription of viral genomes. Nearly half (48.5%) of ∼6.2 million SNPs analyzed in the total sample set contained putative unique Texas alleles. Most of these alleles were likely inherited to subsequent F1 Florida panthers, as these individuals manifested a threefold increase in observed heterozygosity with respect to their immediate, canonical Florida panther predecessors. Demographic simulations were consistent with a recent colonization event in North America by a small number of founders from South America during the last glacial period. In conclusion, we provide an extensive set of genomic resources for pumas and elucidate the genomic effects of genetic rescue on this iconic conservation success story.
Mixing gene pools in translocations can create populations with higher genetic diversity and evolutionary potential compared to single sources. However, the benefits of outcrossing on genetic rescue ...may depend on species' life history, notably mating systems. We assessed outcomes on growth and survival of different kinds of cross in a translocated population of the highly endangered mixed‐mating species Banksia brownii, established from multiple sources. We genetically assigned plants grown from field‐pollinated seed as of selfed, within‐source or between‐source (referring to the original source populations) cross types, and estimated proportion of heterozygous loci for each plant. We modeled the associations among genetic predictors (cross type, level of genetic diversity, and ancestry) and fitness proxies measured in glasshouse and field. At the translocation site, selfing rates were approximately 53–70% and crossing among sources was rare, both likely owing to different patterns of flowering among plants. Offspring of selfed plants were consistently smaller in volume in the glasshouse than were offspring from within‐source crosses. There was no evidence from the first 3 years that survival in the field was influenced by any predictor tested, but the smaller volume of selfed plants in the glasshouse and correlation of glasshouse size at 5 months with the size of the same plants at 3 years in the field suggest that more time may be needed to observe any effects of outcrossing on survival and fitness. Our results highlight the importance of monitoring mating systems, genetic diversity, and fitness data for evaluating translocation success and informing adaptive management.
The current rapid rate of human-driven environmental change presents wild populations with novel conditions and stresses. Theory and experimental evidence for evolutionary rescue present a promising ...case for species facing environmental change persisting via adaptation. Here, we assess the potential for evolutionary rescue in wild vertebrates. Available information on evolutionary rescue was rare and restricted to abundant and highly fecund species that faced severe intentional anthropogenic selective pressures. However, examples from adaptive tracking in common species and genetic rescues in species of conservation concern provide convincing evidence in favour of the mechanisms of evolutionary rescue. We conclude that low population size, long generation times and limited genetic variability will result in evolutionary rescue occurring rarely for endangered species without intervention. Owing to the risks presented by current environmental change and the possibility of evolutionary rescue in nature, we suggest means to study evolutionary rescue by mapping genotype → phenotype → demography → fitness relationships, and priorities for applying evolutionary rescue to wild populations.
Owing to decreasing costs and increased efficiency, it is now conceivable that conservation genomic information can be used to improve the effectiveness of recovery programs for many, if not most, ...threatened plants. We suggest that a simple genomic study be viewed as an initial step in conservation decision-making, as it informs long-term recovery efforts in various ways. We present biodiversity managers and conservation biologists with a simple, standardized workflow for genomic research that can guide efficient collection, analysis and application of genomic information across disparate threatened plants. Using two case studies, ‘Banksia vincentia’ and Daphnandra johnsonii, we demonstrate how a single round of genotyping by sequencing – a one-time cost – produces multiple directly applicable benefits, and how generating genomic information as early as possible can enhance conservation outcomes. We argue for a shift away from asking whether genomic information is needed or justified, and a shift towards consideration of the questions that need to be addressed. Such questions should aimed at cost-effectively guiding multiple practical aspects of a threatened plant’s management plan. The workflow presented here should help relevant stakeholders design a sampling strategy that directly suits their questions and needs.
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•Conservation genomics should be considered a critical initial step in the management of threatened species.•We present a simple workflow that can answer multiple management questions with one single sampling event.•The ensuing analyses provide critical knowledge and understanding of the target species, as well as directly applicable management solution.•This broadly applicable workflow helps stakeholders design a sampling strategy that suits their questions and needs.
The number of predisposing genes is continuously growing with the widespread availability of DNA sequencing, increasing the prevalence of hematologic malignancies with germline predisposition. ...Cytogenetic analyses provide an effective approach for the recognition of these malignancies with germline predisposition, which is critical for proper diagnosis, optimal treatment and genetic counseling.
Based on the World Health Organization and the international consensus classifications as well as the European LeukemiaNet recommendations, this review first presents an advanced classification of neoplasms with germline predisposition focused on the acquired cytogenetic alterations during leukemogenesis.
The various genetic rescue mechanisms and the progression to transformation are then explained. The review also outlines the specific constitutional and somatic cytogenetic aberrations indicative of germline predisposition disorders in B-acute lymphoblastic leukemia (ALL), T-ALL, bone marrow failure syndrome and myeloid neoplasms. An emphasis is made on monosomy 7 in the predisposition field, its frequency and diagnosis impact as well as its various circumstances of occurrence. Lastly, we propose cytogenetic technical recommendations and guidelines for clinical reporting of these specific aberrations.
Research has shown that evolution occurs on the same timescales as changes in population size, and that gene frequency and population dynamics interact with each other. A growing recognition of such ...eco-evolutionary dynamics highlights a need to study how ecological and evolutionary interactions play out on timescales most relevant to conservation and management. However, the roles of evolution in the outcomes of conservation and ecosystem management are not well understood. This review aims to illustrate the importance of considering evolutionary perspectives in conservation ecology when faced with anthropogenic environmental changes such as climate change, habitat fragmentation, and alien species. We describe the fundamental processes underlying evolution and discuss how evolutionary approaches affect conservation outcomes, as well as specific measures and future prospects for improving conservation and ecosystem management.
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