Understanding temporal variation of threats that cause species endangerment is a key to understand conservation strategies needed to improve species recovery. We assessed temporal variation in the threats to species listed under the United States Endangered Species Act (ESA) as identified by the United States Fish and Wildlife Service (USFWS) and National Marine Fisheries Service (NMFS). Based on initial review of ESA listing decisions and literature, we identified six overarching threat categories: habitat modification, overutilization, pollution, species-species interaction, demographic stochasticity, and environmental stochasticity. We screened listing decision documents to determine threat occurrence (i.e., presence/absence of a given threat in a listing decision) for each threat category for all species listed between 1975 and 2017. We evaluated how the number of threats and specific threat occurrences changed over the past four decades. We found that the number of threats per listing decision increased more than twofold from an average of 1.5 (95% CI: 1.3-1.7) threats in 1975 to 3.7 (95% CI: 3.4-4.0) threats in 2017. Threat occurrence increased for habitat modification, environmental stochasticity and species-species interaction, while it decreased for overutilization since 1975 and for demographic stochasticity and pollution since the mid-2000s. The documented increase in number of threats at time of listing may be due to a growing human population exerting increased pressure on species persistence, improved scientific advancement in understanding factors influencing species endangerment, or prolonged time taken for more recent species to be listed under the ESA. We believe that key federal and state governmental regulations have resulted in a documented decrease in overutilization, demographic stochasticity, and pollution, and we recommend large-scale strategies combined with local planning efforts to address the growing threats of habitat loss, environmental stochasticity, and species-species interaction. K E Y W O R D SEndangered Species Act, environmental regulations, policy, temporal, threats Authors after Haines are listed in alphabetical order

American chestnut (Castanea dentata) was once the most economically and ecologically important hardwood species in the eastern United States. In the first half of the 20th century, an exotic fungal pathogen—Cryphonectria parasitica—decimated the species, killing billions of chestnut trees. Two approaches to developing blight‐resistant American chestnut populations show promise, but both will require introduction of adaptive genomic diversity from wild germplasm to produce diverse, locally adapted restoration populations. Here we characterize population structure, demographic history, and genomic diversity in a range‐wide sample of 384 wild American chestnuts to inform conservation and breeding with blight‐resistant varieties. Population structure analyses suggest that the chestnut range can be roughly divided into northeast, central, and southwest populations. Within‐population genomic diversity estimates revealed a clinal pattern with the highest diversity in the southwest, which likely reflects bottleneck events associated with Quaternary glaciation. Finally, we identified genomic regions under positive selection within each population, which suggests that defence against fungal pathogens is a common target of selection across all populations. Taken together, these results show that American chestnut underwent a postglacial expansion from the southern portion of its range leading to three extant genetic populations. These populations will serve as management units for breeding adaptive genetic variation into the blight‐resistant tree populations for targeted reintroduction efforts.

American chestnut (Castanea dentata) was once the most economically and ecologically important hardwood species in the United States. In the first half of the 20th century, an exotic fungal pathogen – Cryphonectria parasitica – decimated the species, killing approximately four billion trees. Two approaches to developing blight resistant American chestnut populations show promise, but both will require introduction of adaptive genomic diversity from wild germplasm to produce diverse, locally adapted reforestation populations. Here we characterize population structure, demographic history, and genomic diversity in a range-wide sample of 384 wild American chestnuts to inform conservation and breeding with blight resistant varieties. Population structure analyses with DAPC and ADMIXTURE suggest that the chestnut range can be roughly divided into northeast, central, and southwest populations. Within-population genomic diversity estimates revealed a clinal pattern with the highest diversity in the southwest, which likely reflects bottleneck events associated with Quaternary glaciation. Finally, we identified genomic regions under positive selection within each population, which suggests that defense against fungal pathogens is a common target of selection across all populations. Taken together, these results show that American chestnut underwent a postglacial expansion from the southern portion of its range leading to three extant populations. These populations will serve as management units for breeding adaptive genetic variation into the blight-resistant tree populations for targeted reintroduction efforts.

The American chestnut (Castanea dentata) is a functionally extinct tree species that was decimated by an invasive fungal pathogen in the early 20thcentury. Disease resistant chestnuts have been developed through hybridization and genetic modification, but these populations may lack the adaptive genomic diversity necessary to restore the species across its climatically diverse historical range. An understanding of the genomic architecture of local adaptation in wild American chestnut and identification of seed zones for germplasm conservation are necessary in order to deploy locally adapted, disease-resistant American chestnut populations. Here, we characterize the genomic basis of climate adaptation in remnant wild American chestnut, define seed zones based on climate envelopes and adaptive diversity, and make sampling recommendations for germplasm conservation. Whole genome re-sequencing of 384 trees coupled with genotype-environment association methods suggest the species range can be most parsimoniously subdivided into three seed zones characterized by relatively homogeneous allele frequencies relative to rangewide adaptive diversity. Using these data, we developed a method to estimate the number of samples required from each seed zone to recapitulate standing adaptive diversity in each seed zone, and found that on average, 21-29 trees will need to be conserved to capture 95% of the wild adaptive diversity. Taken together, these results will inform the development of anex situgermplasm conservation and breeding plan to develop locally adapted blight-resistant American chestnut populations, and provide a blueprint for developing restoration plans for other imperiled tree species.