An official website of the United States government
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
Conservation genetics of Sclerocactus in Colorado: the importance of accurate taxonomy to conservation
IntroductionRecent advances in genetic data collection utilizing next-generation DNA sequencing technologies have the potential to greatly aid the taxonomic assessment of species of conservation concern, particularly species that have been difficult to describe using morphology alone. Accurate taxonomic descriptions aided by genetic data are essential to directing limited conservation resources to species most in need.Sclerocactus glaucusis a plant endemic to Western Colorado that is currently listed as Threatened under the Endangered Species Act (ESA). However, in 2023, the U. S. Fish and Wildlife Service proposed de-listingS. glaucusfrom the ESA due to recovery of the species. Previous research had found substantial genetic structure between populations in the northern part of theS. glaucusrange relative to the majority of the species distribution. MethodsIn this study we utilized double-digest Restriction-site Associated DNA sequencing (RAD-seq) in order to better understand the genetic structure ofS. glaucus. ResultsOur results indicate thatS. glaucuscontains two distinct evolutionary lineages that warrant recognition at the level of species, with what was previously described asS. glaucusNorth being recognized asSclerocactus dawsoniae. DiscussionThe newly describedS. dawsoniaehas a limited estimated number of individuals, low levels of nucleotide diversity, a very narrow geographic range, and an uneven geographic distribution with most plants being found in a single management area, all of which supports continued direct conservation of this species. In contrast,S. glaucushas a large estimated minimum population size, a broad geographic range that includes numerous protected areas, and adequate levels of genetic diversity. Without further conservation action, a delisting decision forS. glaucuswill simultaneously remove all Endangered Species Act protections forS. dawsoniae. The current work demonstrates the importance of having robust genetic datasets when planning conservation activities for species of concern. Moving forward, we recommend that government stakeholders prioritize supporting genetic studies of endangered species prior to making any changes to listing decisions.
more »
« less
- Award ID(s):
- 2322260
- PAR ID:
- 10544458
- Publisher / Repository:
- Frontiers in Conservation Science
- Date Published:
- Journal Name:
- Frontiers in Conservation Science
- Volume:
- 4
- ISSN:
- 2673-611X
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Climate change poses a growing threat to biodiversity, but the welfare consequences of these changes are not well understood. Here we analyze data on the US Endangered Species Act and project increases in species listing and spending due to climate change. We show that higher endangerment is strongly associated with the probability of listing but also find a large bias toward vertebrate species for both listing and spending. Unmitigated warming would cause the listing of an additional 690 species and committed spending of $21 billion by 2100. Several thousand more species would be critically imperiled by climate change but remain unlisted. Finally, we compare ESA spending with estimates of willingness to pay for conservation of 36 listed species. Aggregate WTP is larger than ESA spending for the vast majority of species even using conservative assumptions and typically one to two orders of magnitude larger than direct ESA spending using less restrictive assumptions.more » « less
-
Insights from conservation genomics have dramatically improved recovery plans for numerous endangered species. However, most taxa have yet to benefit from the full application of genomic technologies. The mountain yellow-legged frog species complex, Rana muscosa and Rana sierrae, inhabits the Sierra Nevada mountains and Transverse/Peninsular Ranges of California and Nevada. Both species have declined precipitously throughout their historical distributions. Conservation management plans outline extensive ongoing recovery efforts but are still based on the genetic structure determined primarily using a single mitochondrial sequence. Our study used two different sequencing strategies – amplicon sequencing and exome capture – to refine our understanding of the population genetics of these imperiled amphibians. We used buccal swabs, museum tissue samples, and archived skin swabs to genotype frog populations across their range. Using the amplicon sequencing and exome capture datasets separately and combined, we document five major genetic clusters. Notably, we found evidence supporting previous species boundaries within Kings Canyon National Park with some exceptions at individual sites. Though we see evidence of genetic clustering, especially in the R. muscosa clade, we also found evidence of some admixture across cluster boundaries in the R. sierrae clade, suggesting a stepping-stone model of population structure. We also find that the southern R. muscosa cluster had large runs of homozygosity and the lowest overall heterozygosity of any of the clusters, consistent with previous reports of marked declines in this area. Overall, our results clarify management unit designations across the range of an endangered species and highlight the importance of sampling the entire range of a species, even when collecting genome-scale data.more » « less
-
Abstract AimIntraspecific genetic variation is key for adaptation and survival in changing environments and is known to be influenced by many factors, including population size, dispersal and life‐history traits. We investigated genetic variation within Neotropical amphibian species to provide insights into how natural history traits, phylogenetic relatedness, climatic and geographic characteristics can explain intraspecific genetic diversity. LocationNeotropics. TaxonAmphibians. MethodsWe assembled data sets using open‐access databases for natural history traits, genetic sequences, phylogenetic trees, climatic and geographic data. For each species, we calculated overall nucleotide diversity (π) and tested for isolation by distance (IBD) and isolation by environment (IBE). We then identified predictors ofπ, IBD and IBE using random forest (RF) regression or RF classification. We also fitted phylogenetic generalized linear mixed models (PGLMMs) to predictπ, IBD and IBE. ResultsWe compiled 4052 mitochondrial DNA sequences from 256 amphibian species (230 frogs and 26 salamanders), georeferencing 2477 sequences from 176 species that were not linked to occurrence data. RF regressions and PGLMMs were congruent in identifying range size and precipitation (σ) as the most important predictors ofπ, influencing it positively. RF classification and PGLMMs identified minimum elevation as an important predictor of IBD; most species without IBD tended to occur at higher elevations. Maximum latitude and precipitation (σ) were the best predictors of IBE, and most species without IBE occur at lower latitudes and in areas with more variable precipitation. Main ConclusionsThis study identified predictors of genetic variation in Neotropical amphibians using both machine learning and phylogenetic methods. This approach was valuable to determine which predictors were congruent between methods. We found that species with small ranges or living in zones with less variable precipitation tended to have low genetic diversity. We also showed that Western Mesoamerica, Andes and Atlantic Forest biogeographic units harbour high diversity across many species that should be prioritized for protection. These results could play a key role in the development of conservation strategies for Neotropical amphibians.more » « less
-
Abstract Ongoing declines in insect populations have led to substantial concern and calls for conservation action. However, even for relatively well studied groups, like butterflies, information relevant to species‐specific status and risk is scattered across field guides, the scientific literature, and agency reports. Consequently, attention and resources have been spent on a minuscule fraction of insect diversity, including a few well studied butterflies. Here we bring together heterogeneous sources of information for 396 butterfly species to provide the first regional assessment of butterflies for the 11 western US states. For 184 species, we use monitoring data to characterize historical and projected trends in population abundance. For another 212 species (for which monitoring data are not available, but other types of information can be collected), we use exposure to climate change, development, geographic range, number of host plants, and other factors to rank species for conservation concern. A phylogenetic signal is apparent, with concentrations of declining and at‐risk species in the families Lycaenidae and Hesperiidae. A geographic bias exists in that many species that lack monitoring data occur in the more southern states where we expect that impacts of warming and drying trends will be most severe. Legal protection is rare among the taxa with the highest risk values: of the top 100 species, one is listed as threatened under the US Endangered Species Act and one is a candidate for listing. Among the many taxa not currently protected, we highlight a short list of species in decline, including Vanessa annabella , Thorybes mexicanus , Euchloe ausonides , and Pholisora catullus . Notably, many of these species have broad geographic ranges, which perhaps highlights a new era of insect conservation in which small or fragmented ranges will not be the only red flags that attract conservation attention.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript
- Journal Article:
- https://doi.org/10.3389/fcosc.2023.1310985
