An official website of the United States government
ABSTRACT Restoring connectivity via assisted migration is a useful but currently underused approach for maintaining genetic diversity and preventing extirpations of threatened species. The use of assisted migration as a conservation strategy may be limited by the difficulty of balancing the benefits of reconnecting populations (including reduced inbreeding depression and increased adaptive capacity) with the perceived risk of outbreeding depression, which requires comprehensive knowledge of the landscape of adaptive, neutral, deleterious, and structural variation across a species' range. Using a combination of reduced‐representation and whole‐genome sequencing, we characterized genomic diversity and differentiation for the Arkansas Darter (Etheostoma cragini) across its range in the Midwestern US. We found strong population structure and large differences in genetic diversity and effective population sizes across drainages. The strength of genetic isolation by river distance differed among drainages, with landscape type surrounding streams and impoundments also contributing to genetic isolation. Despite low effective population sizes in some populations, there was surprisingly little evidence for recent inbreeding (based on the absence of long runs of homozygosity) or for elevated levels of deleterious variation in smaller populations. Considering neutral, adaptive, deleterious, and structural variation allowed us to identify several potential recipient populations that may benefit from translocations and potential donor sites throughout the range. Planning translocation strategies intended for restored connectivity and possible genetic rescue at earlier stages in species decline will likely increase the probability of retaining genetic diversity and population persistence over the long term while minimizing risks associated with translocation.
more »
« less
Recently Delisted Songbird Harbors Extensive Genomic Evidence of Inbreeding, Potentially Complicating Future Recovery
The Kirtland's warbler (Setophaga kirtlandi) is a rare migratory passerine species and habitat specialist of the North American Jack Pine Forests. Their near extinction in the 1970s classified them as endangered and protected under the Endangered Species Act of 1973. After decades of intense conservation management, their population size recovered, and they were delisted from federal protection in 2019. We explore the genomic consequences of this harsh bottleneck and recovery by comparing the genomic architecture of two closely related species whose population sizes have remained large and stable, Hooded Warblers (Setophaga citrina) and American Redstarts (Setophaga ruticilla). We used whole‐genome sequencing to characterize the distribution of runs of homozygosity and deleterious genetic variation. We find evidence that Kirtland's warblers exhibit genetic patterns consistent with recent inbreeding. Our results also show that Kirtland's warblers carry an excess proportion of deleterious variation, which could complicate management for this conservation‐reliant species. This analysis provides a genetically informed perspective that should be thoroughly considered when delisting other species from federal protections. Through the increasing accessibility of genome sequencing technology, it will be more feasible to monitor the genetic landscape of recovering populations to ensure their long‐term survival independent of conservation intervention.
more »
« less
- Award ID(s):
- 2131469
- PAR ID:
- 10564576
- Publisher / Repository:
- Wiley
- Date Published:
- Journal Name:
- Evolutionary Applications
- Volume:
- 17
- Issue:
- 12
- ISSN:
- 1752-4571
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
ABSTRACT Wildlife trafficking poses a major threat to biodiversity, particularly for species like parrots that are targeted in the pet trade. The Yellow‐headed Parrot (Amazona oratrix), an endangered species native to Mexico and Central America, is frequently poached from unknown geographic locations, hindering the identification of smuggling sources and repatriation of any confiscated individuals. Here, we used population genomic tools to determine the source of 18 Yellow‐headed Parrots confiscated as nestlings during a 2021 U.S.–Mexico border crossing into California. To build a genomic reference map, we extracted and sequenced DNA derived from the toe pads of historical museum specimens from across the range of three out of the four describedA. oratrixsubspecies. Genomic data revealed that the three sequenced subspecies correspond to unique ancestry groups and revealed a substantial genetic divide between Pacific and Atlantic coastal populations ofA. o. oratrix. The smuggled parrots and parrots from the introduced population in southern California both consistently clustered with eastern populations ofA. o. oratrixin genomic analyses. Concordantly, the predicted origin of these smuggled birds was eastern Mexico, based on the genomic reference map derived from historical samples. Kinship analysis reveals multiple cases of sibling‐level relationships among the smuggled birds, suggesting that wildA. oratrixnests continue to be raided for the pet trade despite the species' endangered status. Overall, this study illustrates the power of using museum genomics to trace wildlife trafficking routes, inform conservation policy, and improve taxonomic resolution in species of conservation concern.more » « less
-
ABSTRACT. Urbanisation has led to increasing homogenization of plant communities across cities. However, it is unclear whether these patterns extend to cosmopolitan plant species at the genetic level. We examined genome‐wide genetic patterns in six widespread plant species (three Poaceae and three Asteraceae) across five cities in the USA (Boston, Baltimore, Minneapolis‐St. Paul, Phoenix, and Los Angeles) using reduced‐representation sequencing. We assessed genetic structure, differentiation, and patterns of isolation by distance (IBD) and environment (IBE) to determine if species were genetically homogeneous or differentiated by city, percentage of impervious surface, or both. Most species exhibited limited population structure overall, withPoa annua(annual bluegrass),Taraxacum officinale(dandelion), andCynodon dactylon(Bermuda grass) showing no significant genetic differentiation among cities, a pattern consistent with high gene flow mediated by human activity. Notable exceptions included city‐level differences inErigeron canadensis(horseweed) andLactuca serriola(prickly lettuce), especially in Phoenix. We also observed low genetic diversity inDigitaria sanguinalis(crabgrass) from Phoenix, suggesting recent founder effects or selection via environmental filtering.Erigeron canadensis,the only native species studied, displayed stronger differentiation by city, along with significant isolation by temperature and distance. Among all species, we found no evidence for population structure by impervious surface. Our findings indicate that widespread population genetic structure patterns of cosmopolitan plants are likely to depend more on species attributes (e.g., self‐compatibility) and human‐mediated dispersal than on urbanisation per se.more » « less
-
ABSTRACT Management strategies, such as assisted gene flow, can increase resilience to climate change in tree populations. Knowledge of evolutionary history and genetic structure of species are needed to assess the risks and benefits of different strategies.Quercus tomentella, or Island Oak, is a rare oak restricted to six Channel Islands in California, United States, and Baja California, Mexico. Previous work has shown that Island Oaks on each island are genetically differentiated, but it is unclear whether assisted gene flow could enable populations to tolerate future climates. We performed whole‐genome sequencing on Island Oak individuals andQ. chrysolepis, a closely related species that hybridizes with Island Oak (127 total), to characterize genetic structure and introgression across its range and assess the relationship between genomic variation and climate. We introduce and assess three potential management strategies with different trade‐offs between conserving historic genetic structure and enabling populations to survive changing climates: the status quo approach; ecosystem preservation approach, which conserves the trees and their associated biodiversity; and species preservation approach, which conserves the species. We compare the impact of these approaches on predicted maladaptation to climate using Gradient Forest. We also introduce a climate suitability index to identify optimal pairs of seed sources and planting sites for approaches involving assisted gene flow. We found one island (Santa Rosa) that could benefit from the ecosystem preservation approach and also serve as a species preservation site. Overall, we find that both the ecosystem and species preservation approaches will do better than the status quo approach. If preserving Island Oak ecosystems is the goal, assisted dispersal into multiple sites could produce adapted populations. If the goal is to preserve a species, the Santa Rosa population would be suitable. This case study both illustrates viable conservation strategies for Island Oak and introduces a framework for tree conservation.more » « less
-
ABSTRACT The rate of input of new genetic mutations, and the rate at which that variation is reshuffled, are key evolutionary processes shaping genomic diversity. Importantly, these rates vary not just across populations and species but also across individual genomes. Despite previous studies having demonstrated that failing to account for rate heterogeneity across the genome can bias the inference of both selective and neutral population genetic processes, mutation and recombination rate maps have to date only been generated for a relatively small number of organisms. Here, we infer such fine‐scale maps for the aye‐aye (Daubentonia madagascariensis)—a highly endangered strepsirrhine that represents one of the earliest splits in the primate clade and thus stands as an important outgroup to the more commonly studied haplorrhines—utilizing a recently released fully annotated genome combined with high‐quality population sequencing data. We compare our indirectly inferred rates to previous pedigree‐based estimates, finding further evidence of relatively low mutation and recombination rates in aye‐ayes compared to other primates.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript
- Journal Article:
- https://doi.org/10.1111/eva.70052
