{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T21:58:14Z","timestamp":1790459894357,"version":"4.1.0"},"reference-count":114,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2020,7,12]],"date-time":"2020-07-12T00:00:00Z","timestamp":1594512000000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100008982","name":"National Science Foundation","doi-asserted-by":"publisher","award":["1655694"],"award-info":[{"award-number":["1655694"]}],"id":[{"id":"10.13039\/501100008982","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Trait loss represents an intriguing evolutionary problem, particularly when it occurs across independent lineages. Fishes in light-poor environments often evolve \u201ctroglomorphic\u201d traits, including reduction or loss of both pigment and eyes. Here, we investigate the genomic basis of trait loss in a blind and depigmented African cichlid, Lamprologus lethops, and explore evolutionary forces (selection and drift) that may have contributed to these losses. This species, the only known blind cichlid, is endemic to the lower Congo River. Available evidence suggests that it inhabits deep, low-light habitats. Using genome sequencing, we show that genes related to eye formation and pigmentation, as well as other traits associated with troglomorphism, accumulated inactivating mutations rapidly after speciation. A number of the genes affected in L.\u00a0lethops are also implicated in troglomorphic phenotypes in Mexican cavefish (Astyanax mexicanus) and other species. Analysis of heterozygosity patterns across the genome indicates that L.\u00a0lethops underwent a significant population bottleneck roughly 1 Ma, after which effective population sizes remained low. Branch-length tests on a subset of genes with inactivating mutations show little evidence of directional selection; however, low overall heterozygosity may reduce statistical power to detect such signals. Overall, genome-wide patterns suggest that accelerated genetic drift from a severe bottleneck, perhaps aided by directional selection for the loss of physiologically expensive traits, caused inactivating mutations to fix rapidly in this species.<\/jats:p>","DOI":"10.1093\/gbe\/evaa144","type":"journal-article","created":{"date-parts":[[2020,7,6]],"date-time":"2020-07-06T19:11:02Z","timestamp":1594062662000},"page":"1392-1406","source":"Crossref","is-referenced-by-count":26,"title":["Genomic Analysis of the Only Blind Cichlid Reveals Extensive Inactivation in Eye and Pigment Formation Genes"],"prefix":"10.1093","volume":"12","author":[{"given":"Matthew L","family":"Aardema","sequence":"first","affiliation":[{"name":"Department of Biology, Montclair State University"},{"name":"Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melanie L J","family":"Stiassny","sequence":"additional","affiliation":[{"name":"Department of Ichthyology, American Museum of Natural History, New York, New York"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S Elizabeth","family":"Alter","sequence":"additional","affiliation":[{"name":"Department of Ichthyology, American Museum of Natural History, New York, New York"},{"name":"The Graduate Center, City University of New York"},{"name":"Department of Biology, York College\/The City University of New York"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,7,11]]},"reference":[{"issue":"Suppl 2","key":"2020092005542024100_evaa144-B1","doi-asserted-by":"crossref","first-page":"W7","DOI":"10.1093\/nar\/gkq291","article-title":"TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations","volume":"38","author":"Abascal","year":"2010","journal-title":"Nucleic Acids 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