scholarly journals Mountain lion genomes provide insights into genetic rescue of inbred populations

2018 ◽  
Author(s):  
Nedda F. Saremi ◽  
Megan A. Supple ◽  
Ashley Byrne ◽  
James A. Cahill ◽  
Luiz Lehmann Coutinho ◽  
...  
Keyword(s):  
Landscape Connectivity ◽  
Geographic Range ◽  
Long Term Effects ◽  
Genetic Rescue ◽  
Isolated Populations ◽  
Mountain Lions ◽  
Mountain Lion ◽  
Genome Wide ◽  
Inbred Populations ◽  
North And South America

Introduction paragraph/AbstractAcross the geographic range of mountain lions, which includes much of North and South America, populations have become increasingly isolated due to human persecution and habitat loss. To explore the genomic consequences of these processes, we assembled a high-quality mountain lion genome and analyzed a panel of resequenced individuals from across their geographic range. We found strong geographical structure and signatures of severe inbreeding in all North American populations. Tracts of homozygosity were rarely shared among populations, suggesting that assisted gene flow would restore local genetic diversity. However, the genome of an admixed Florida panther that descended from a translocated individual from Central America had surprisingly long tracts of homozygosity, indicating that genomic gains from translocation were quickly lost by local inbreeding. Thus, to sustain diversity, genetic rescue will need to occur at regular intervals, through repeated translocations or restoring landscape connectivity. Mountain lions provide a rare opportunity to examine the potential to restore diversity through genetic rescue, and to observe the long-term effects of translocation. Our methods and results provide a framework for genome-wide analyses that can be applied to the management of small and isolated populations.

scholarly journals Puma genomes from North and South America provide insights into the genomic consequences of inbreeding

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Nedda F. Saremi ◽  
Megan A. Supple ◽  
Ashley Byrne ◽  
James A. Cahill ◽  
Luiz Lehmann Coutinho ◽  
...  
Keyword(s):  
North American ◽  
Landscape Connectivity ◽  
Western Hemisphere ◽  
Central American ◽  
South American ◽  
Isolated Populations ◽  
Genome Wide ◽  
North And South America ◽  
North And South ◽  
Close Inbreeding

Abstract Pumas are the most widely distributed felid in the Western Hemisphere. Increasingly, however, human persecution and habitat loss are isolating puma populations. To explore the genomic consequences of this isolation, we assemble a draft puma genome and a geographically broad panel of resequenced individuals. We estimate that the lineage leading to present-day North American pumas diverged from South American lineages 300–100 thousand years ago. We find signatures of close inbreeding in geographically isolated North American populations, but also that tracts of homozygosity are rarely shared among these populations, suggesting that assisted gene flow would restore local genetic diversity. The genome of a Florida panther descended from translocated Central American individuals has long tracts of homozygosity despite recent outbreeding. This suggests that while translocations may introduce diversity, sustaining diversity in small and isolated populations will require either repeated translocations or restoration of landscape connectivity. Our approach provides a framework for genome-wide analyses that can be applied to the management of similarly small and isolated populations.

scholarly journals Genomic signatures of inbreeding and genetic load in a threatened rattlesnake

2021 ◽  
Author(s):  
Alexander Ochoa ◽  
H. Lisle Gibbs
Keyword(s):  
Threatened Species ◽  
Empirical Studies ◽  
Genetic Load ◽  
Population History ◽  
Deleterious Mutations ◽  
Genetic Rescue ◽  
Isolated Populations ◽  
Genome Wide ◽  
The Impact

Theory predicts that threatened species living in small populations will experience high levels of inbreeding that will increase their negative genetic load but recent work suggests that the impact of load may be minimized by purging resulting from long term population bottlenecks. Empirical studies that examine this idea using genome-wide estimates of inbreeding and genetic load in threatened species are limited. Here we use genome resequencing data to compare levels of inbreeding, levels of genetic load and population history in threatened Eastern massasauga rattlesnakes (Sistrurus catenatus) which exist in small isolated populations and closely-related yet outbred Western massasauga rattlesnakes (S. tergeminus). In terms of inbreeding, S. catenatus genomes had a greater number of ROHs of varying sizes indicating sustained inbreeding through repeated bottlenecks when compared to S. tergeminus. At the species level, outbred S. tergeminus had higher genome-wide levels of genetic load in the form of greater numbers of derived deleterious mutations compared to S. catenatus presumably due to long-term purging of deleterious mutations in S. catenatus. In contrast, mutations that escaped the “drift sieve” and were polymorphic within S. catenatus populations were more abundant and more often found in homozygote genotypes than in S. tergeminus suggesting a reduced efficiency of purifying selection in smaller S. catenatus populations. Our results support an emerging idea that the historical demography of a threatened species has a significant impact on the type of genetic load present which impacts implementation of conservation actions such as genetic rescue.

scholarly journals Low Persistence of Genetic Rescue Across Generations in the Arctic Fox (Vulpes lagopus)

2021 ◽  
Author(s):  
Anna Lotsander ◽  
Malin Hasselgren ◽  
Malin Larm ◽  
Johan Wallén ◽  
Anders Angerbjörn ◽  
...  
Keyword(s):  
Time Perspective ◽  
Chromosome Analysis ◽  
Small Population ◽  
The Arctic ◽  
Vulpes Lagopus ◽  
Long Term Effects ◽  
Genetic Rescue ◽  
Isolated Populations ◽  
Individual Fitness

Abstract Genetic rescue can facilitate the recovery of small and isolated populations suffering from inbreeding depression. Long-term effects are however complex, and examples spanning over multiple generations under natural conditions are scarce. The aim of this study was to test for long-term effects of natural genetic rescue in a small population of Scandinavian Arctic foxes (Vulpes lagopus). By combining a genetically verified pedigree covering almost 20 years with a long-term dataset on individual fitness (n = 837 individuals), we found no evidence for elevated fitness in immigrant F2 and F3 compared to native inbred foxes. Population inbreeding levels showed a fluctuating increasing trend and emergence of inbreeding within immigrant lineages shortly after immigration. Between 0–5 and 6–9 years post immigration, the average number of breeding adults decreased by almost 22% and the average proportion of immigrant ancestry rose from 14% to 27%. Y chromosome analysis revealed that 2 out of 3 native male lineages were lost from the gene pool, but all founders represented at the time of immigration were still contributing to the population at the end of the study period through female descendants. The results highlight the complexity of genetic rescue and suggest that beneficial effects can be brief. Continuous gene flow may be needed for small and threatened populations to recover and persist in a longer time perspective.

scholarly journals An evolutionary perspective on contemporary genetic load in threatened species to inform future conservation efforts

2021 ◽  
Author(s):  
Samarth Mathur ◽  
John Tomeček ◽  
Luis Tarango-Arámbula ◽  
Robert Perez ◽  
Andrew DeWoody
Keyword(s):  
Population Genomics ◽  
Empirical Distribution ◽  
Demographic History ◽  
Genetic Load ◽  
Purifying Selection ◽  
Deleterious Mutations ◽  
Genetic Rescue ◽  
Isolated Populations ◽  
Potential Donor ◽  
Inbred Populations

In theory, genomic erosion can be reduced in fragile “recipient” populations by translocating individuals from genetically diverse “donor” populations. However, recent simulation studies have argued that such translocations can, in principle, serve as a conduit for new deleterious mutations to enter recipient populations. A reduction in evolutionary fitness is associated with a higher load of deleterious mutations and thus, a better understanding of evolutionary processes driving the empirical distribution of deleterious mutations is crucial. Here, we show that genetic load is evolutionarily dynamic in nature and that demographic history greatly influences the distribution of deleterious mutations over time. Our analyses, based on both demographically explicit simulations as well as whole genome sequences of potential donor-recipient pairs of Montezuma Quail (Cyrtonyx montezumae) populations, indicate that all populations tend to lose deleterious mutations during bottlenecks, but that genetic purging is pronounced in smaller populations with stronger bottlenecks. Despite carrying relatively fewer deleterious mutations, we demonstrate how small, isolated populations are more likely to suffer inbreeding depression as deleterious mutations that escape purging are homogenized due to drift, inbreeding, and ineffective purifying selection. We apply a population genomics framework to showcase how the phylogeography and historical demography of a given species can enlighten genetic rescue efforts. Our data suggest that small, inbred populations should benefit the most when assisted gene flow stems from genetically diverse donor populations that have the lowest proportion of deleterious mutations.

scholarly journals Development of a 95 SNP Panel To Individually Genotype Mountain Lions (Puma Concolor) For Microfluidic and Other Genotyping Platforms

2021 ◽  
Author(s):  
Michael Buchalski ◽  
Benjamin Sacks ◽  
Kristen Ahrens ◽  
Kyle Gustafson ◽  
Jaime Rudd ◽  
...  
Keyword(s):  
Southern California ◽  
Puma Concolor ◽  
Snp Markers ◽  
Individual Identification ◽  
Illumina Hiseq ◽  
Mountain Lions ◽  
Mountain Lion ◽  
Marker Selection ◽  
Large Predators ◽  
Inbred Populations

Abstract The mountain lion (Puma concolor) is one of the few remaining large predators in California, USA with density estimation from fecal genotypes becoming an essential component of conservation and management. In highly urbanized southern California, mountain lions are fragmented into small, inbred populations making proper marker selection critical for individual identification. We developed a panel of single nucleotide polymorphism (SNP) markers that can be used for consistent, routine mountain lion monitoring by different laboratories. We used a subset of existing Illumina HiSeq data for 104 individuals from throughout California to design a single, highly heterozygous multiplex of 95 SNPs for the Fluidigm platform. This panel confidently differentiates individual mountain lions, identifies sex, and discriminates mountain lions from bobcats. The panel performed well on fecal DNA extracts and based on design, had sufficient resolution to differentiate individual genotypes in even the population with lowest genetic diversity in southern California.

Are there populations suffering genetic erosion that would benefit from augmented gene flow?

2017 ◽  
Author(s):  
Richard Frankham ◽  
Jonathan D. Ballou ◽  
Katherine Ralls ◽  
Mark D. B. Eldridge ◽  
Michele R. Dudash ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Erosion ◽  
Genetic Rescue ◽  
Isolated Populations

Having identified small geographically and genetically isolated populations, we need to determine whether they are suffering genetic erosion, and if so, whether there are any other populations to which they could be crossed. We should next ask whether crossing is expected to be harmful or beneficial, and if beneficial, whether the benefits would be large enough to justify a genetic rescue attempt. Here, we address these questions based on the principles established in the preceding chapters.

Genetic rescue by augmenting gene flow

2017 ◽  
Author(s):  
Richard Frankham ◽  
Jonathan D. Ballou ◽  
Katherine Ralls ◽  
Mark D. B. Eldridge ◽  
Michele R. Dudash ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Inbreeding Coefficient ◽  
Outbreeding Depression ◽  
Genetic Rescue ◽  
Evolutionary Potential ◽  
Beneficial Effects ◽  
The Difference ◽  
Inbred Populations ◽  
Harmful Effects

Inbreeding is reduced and genetic diversity enhanced when a small isolated inbred population is crossed to another unrelated population. Crossing can have beneficial or harmful effects on fitness, but beneficial effects predominate, and the risks of harmful ones (outbreeding depression) can be predicted and avoided. For crosses with a low risk of outbreeding depression, there are large and consistent benefits on fitness that persist across generations in outbreeding species. Benefits are greater in species that naturally outbreed than those that inbreed, and increase with the difference in inbreeding coefficient between crossed and inbred populations in mothers and zygotes. However, benefits are similar across invertebrates, vertebrates and plants. There are also important benefits for evolutionary potential of crossing between populations.

scholarly journals Mountain lion ( Puma concolor ) feeding behavior in the Little Missouri Badlands of North Dakota

2015 ◽  
Vol 97 (2) ◽  
pp. 373-385 ◽  
Author(s):  
David T. Wilckens ◽  
Joshua B. Smith ◽  
Stephanie A. Tucker ◽  
Daniel J. Thompson ◽  
Jonathan A. Jenks
Keyword(s):  
North Dakota ◽  
Puma Concolor ◽  
Feeding Habits ◽  
Total Biomass ◽  
Mountain Lions ◽  
Mountain Lion ◽  
Gps Collars ◽  
The North ◽  
Kill Rate ◽  
Prey Populations

Abstract Recent recolonization of mountain lions ( Puma concolor ) into the Little Missouri Badlands of North Dakota has led to questions regarding the potential impacts of predation on prey populations in the region. From 2012 to 2013, we deployed 9 real-time GPS collars to investigate mountain lion feeding habits. We monitored mountain lions for 1,845 telemetry-days, investigated 506 GPS clusters, and identified 292 feeding events. Deer ( Odocoileus spp.) were the most prevalent item in mountain lion diets (76.9%). We used logistic regression to predict feeding events and size of prey consumed at an additional 535 clusters. Our top model for predicting presence of prey items produced a receiver operating characteristic score of 0.90 and an overall accuracy of 81.4%. Application of our models to all GPS clusters resulted in an estimated ungulate kill rate of 1.09 ungulates/week (95% confidence interval [ CI ] = 0.83–1.36) in summer (15 May‒15 November) and 0.90 ungulates/week (95% CI = 0.69–1.12) in winter (16 November‒14 May). Estimates of total biomass consumed were 5.8kg/day (95% CI = 4.7–6.9) in summer and 7.2kg/day (95% CI = 5.3–9.2) in winter. Overall scavenge rates were 3.7% in summer and 11.9% in winter. Prey composition included higher proportions of nonungulates in summer (female = 21.5%; male = 24.8%) than in winter (female = 4.8%; male = 7.5%). Proportion of juvenile ungulates in mountain lion diets increased during the fawning season (June‒August) following the ungulate birth pulse in June (June–August = 60.7%, 95% CI = 43.0–78.3; September–May = 37.2%, 95% CI = 30.8–43.7), resulting in an ungulate kill rate 1.61 times higher (1.41 ungulates/week, 95% CI = 1.12–1.71) than during the remainder of the year (0.88 ungulates/week, 95% CI = 0.62–1.13). Quantifying these feeding characteristics is essential to assessing the potential impacts of mountain lions on prey populations in the North Dakota Badlands, where deer dominate the available prey base and mountain lions represent the lone apex predator.

Inbreeding and Inbreeding Depression

2020 ◽  
Author(s):  
Donald M. Waller ◽  
Lukas F. Keller
Keyword(s):  
Genetic Variation ◽  
Inbreeding Depression ◽  
Charles Darwin ◽  
Extinction Risk ◽  
Random Mating ◽  
Genetic Material ◽  
Great Length ◽  
Genetic Rescue ◽  
Isolated Populations ◽  
Genetic Transmission

Inbreeding (also referred to as “consanguinity”) occurs when mates are related to each other due to incest, assortative mating, small population size, or population sub-structuring. Inbreeding results in an excess of homozygotes and hence a deficiency of heterozygotes. This, in turn, exposes recessive genetic variation otherwise hidden by heterozygosity with dominant alleles relative to random mating. Interest in inbreeding arose from its use in animal and plant breeding programs to expose such variation and to fix variants in genetically homogenous lines. Starting with Gregor Mendel’s experiments with peas, geneticists have widely exploited inbreeding as a research tool, leading R. C. Lewontin to conclude that “Every discovery in classical and population genetics has depended on some sort of inbreeding experiment” (see Lewontin’s 1965 article “The Theory of Inbreeding.” Science 150:1800–1801). Charles Darwin wrote an entire book on the effects of inbreeding as measured in fifty-two taxa of plants. He and others noted that most plants and animals go to great length to avoid inbreeding, suggesting that inbreeding has high costs that often outweigh the benefits of inbreeding. Benefits of inbreeding include increased genetic transmission while the costs of inbreeding manifest as inbreeding depression when deleterious, mostly recessive alleles otherwise hidden as heterozygotes emerge in homozygote form upon inbreeding. Inbreeding also reduces fitness when heterozygotes are more fit than both homozygotes, but such overdominance is rare. Recurrent mutation continuously generates deleterious recessive alleles that create a genetic “load” of deleterious mutations mostly hidden within heterozygotes in outcrossing populations. Upon inbreeding, the load is expressed when deleterious alleles segregate as homozygotes, causing often substantial inbreeding depression. Although inbreeding alone does not change allele frequencies, it does redistribute genetic variation, reducing it within families or populations while increasing it among families or populations. Inbreeding also increases selection by exposing deleterious recessive mutations, a process called purging that can deplete genetic variation. For all these reasons, inbreeding is a central concept in evolutionary biology. Inbreeding is also central to conservation biology as small and isolated populations become prone to inbreeding and thus suffer inbreeding depression. Inbreeding can reduce population viability and increase extinction risk by reducing individual survival and/or reproduction. Such effects can often be reversed, however, by introducing new genetic material that re-establishes heterozygosity (“genetic rescue”). The current availability of DNA sequence and expression data is now allowing more detailed analyses of the causes and evolutionary consequences of inbreeding.

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