Test Environmental Research Collection

Permanent URI for this collection

https://hdl.handle.net/1911/118256
This is a test collection created as part of a Fondren Fellows project (2024-2025). This collection is intended to serve as a proof of concept for a permanent collection that showcases environmental research conducted by Rice researchers. All items currently in this collection have been mapped from other collections in R-3.

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Browsing Test Environmental Research Collection by Author "Aiden, Erez Lieberman"

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    A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of “Genetic Purging” and Genomic Stability
    (MDPI, 2022) Mohr, David W.; Gaughran, Stephen J.; Paschall, Justin; Naguib, Ahmed; Pang, Andy Wing Chun; Dudchenko, Olga; Aiden, Erez Lieberman; Church, Deanna M.; Scott, Alan F.; Center for Theoretical Biological Physics
    The Hawaiian monk seal (HMS) is the single extant species of tropical earless seals of the genus Neomonachus. The species survived a severe bottleneck in the late 19th century and experienced subsequent population declines until becoming the subject of a NOAA-led species recovery effort beginning in 1976 when the population was fewer than 1000 animals. Like other recovering species, the Hawaiian monk seal has been reported to have reduced genetic heterogeneity due to the bottleneck and subsequent inbreeding. Here, we report a chromosomal reference assembly for a male animal produced using a variety of methods. The final assembly consisted of 16 autosomes, an X, and portions of the Y chromosomes. We compared variants in this animal to other HMS and to a frequently sequenced human sample, confirming about 12% of the variation seen in man. To confirm that the reference animal was representative of the HMS, we compared his sequence to that of 10 other individuals and noted similarly low variation in all. Variation in the major histocompatibility (MHC) genes was nearly absent compared to the orthologous human loci. Demographic analysis predicts that Hawaiian monk seals have had a long history of small populations preceding the bottleneck, and their current low levels of heterozygosity may indicate specialization to a stable environment. When we compared our reference assembly to that of other species, we observed significant conservation of chromosomal architecture with other pinnipeds, especially other phocids. This reference should be a useful tool for future evolutionary studies as well as the long-term management of this species.
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    Genome-wide diversity in the California condor tracks its prehistoric abundance and decline
    (Elsevier, 2021) Robinson, Jacqueline A.; Bowie, Rauri C. K.; Dudchenko, Olga; Aiden, Erez Lieberman; Hendrickson, Sher L.; Steiner, Cynthia C.; Ryder, Oliver A.; Mindell, David P.; Wall, Jeffrey D.; Center for Theoretical and Biological Physics
    Due to their small population sizes, threatened and endangered species frequently suffer from a lack of genetic diversity, potentially leading to inbreeding depression and reduced adaptability.1 During the latter half of the twentieth century, North America’s largest soaring bird,2 the California condor (Gymnogyps californianus; Critically Endangered3), briefly went extinct in the wild. Though condors once ranged throughout North America, by 1982 only 22 individuals remained. Following decades of captive breeding and release efforts, there are now >300 free-flying wild condors and ∼200 in captivity. The condor’s recent near-extinction from lead poisoning, poaching, and loss of habitat is well documented,4 but much about its history remains obscure. To fill this gap and aid future management of the species, we produced a high-quality chromosome-length genome assembly for the California condor and analyzed its genome-wide diversity. For comparison, we also examined the genomes of two close relatives: the Andean condor (Vultur gryphus; Vulnerable3) and the turkey vulture (Cathartes aura; Least Concern3). The genomes of all three species show evidence of historic population declines. Interestingly, the California condor genome retains a high degree of variation, which our analyses reveal is a legacy of its historically high abundance. Correlations between genome-wide diversity and recombination rate further suggest a history of purifying selection against linked deleterious alleles, boding well for future restoration. We show how both long-term evolutionary forces and recent inbreeding have shaped the genome of the California condor, and provide crucial genomic resources to enable future research and conservation.