{"entity": "researcher", "timestamp": "2026-09-23T15:10:32.646Z", "family": "Foley", "given": "Kathleen", "initials": "K", "orcid": "0000-0003-0923-1326", "affiliations": ["College of Law, University of Iowa, Iowa City, IA 52242, USA.", "Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/907a734d325d4f76bf083c68202f2e05.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/907a734d325d4f76bf083c68202f2e05"}}, "publications": [{"entity": "publication", "iuid": "0588b65dcdd14e4084e68dbbef556a0f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0588b65dcdd14e4084e68dbbef556a0f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0588b65dcdd14e4084e68dbbef556a0f"}}, "title": "The contribution of historical processes to contemporary extinction risk in placental mammals.", "authors": [{"family": "Wilder", "given": "Aryn P", "initials": "AP", "orcid": "0000-0003-4970-6891", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5b080282d4674df1bde072812bf448be.json"}}, {"family": "Supple", "given": "Megan A", "initials": "MA", "orcid": "0000-0002-0204-7852", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/073a9fab924c4e96973f1e23accaa7ae.json"}}, {"family": "Subramanian", "given": "Ayshwarya", "initials": "A", "orcid": "0000-0002-4134-7612", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dda9998955294a798208e67cac6baaea.json"}}, {"family": "Mudide", "given": "Anish", "initials": "A", "orcid": "0000-0002-6174-2345", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1bf10150429a444186df7ddf697369e6.json"}}, {"family": "Swofford", "given": "Ross", "initials": "R", "orcid": "0000-0003-3676-8479", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/85b0174c633b417b933092763175bb1c.json"}}, {"family": "Serres-Armero", "given": "Aitor", "initials": "A"}, {"family": "Steiner", "given": "Cynthia", "initials": "C", "orcid": "0000-0002-2131-8072", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9386c16bd7e14ddca60e03e06f6808fe.json"}}, {"family": "Koepfli", "given": "Klaus-Peter", "initials": "KP"}, {"family": "Genereux", "given": "Diane P", "initials": "DP", "orcid": "0000-0001-5770-0989", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/352ee25047c544aaa486a69e7e3333fc.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/612a779b69494f1ca9b6c5f1d84fd711.json"}}, {"family": "Marques-Bonet", "given": "Tomas", "initials": "T", "orcid": "0000-0002-5597-3075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1091cb5bfe394d459969d24bb1c22c66.json"}}, {"family": "Munoz Fuentes", "given": "Violeta", "initials": "V", "orcid": "0000-0003-3574-546X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a5d067d41a846f9bee05b1bdacc1a7f.json"}}, {"family": "Foley", "given": "Kathleen", "initials": "K", "orcid": "0000-0003-0923-1326", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/907a734d325d4f76bf083c68202f2e05.json"}}, {"family": "Meyer", "given": "Wynn K", "initials": "WK", "orcid": "0000-0001-7978-3877", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b1fba9de46a4c8c8cbbbec685a9b94c.json"}}, {"family": "Zoonomia Consortium\u2021", "given": "", "initials": ""}, {"family": "Ryder", "given": "Oliver A", "initials": "OA", "orcid": "0000-0003-2427-763X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d18635ed6fa42d4bbcfddadae70e308.json"}}, {"family": "Shapiro", "given": "Beth", "initials": "B", "orcid": "0000-0002-2733-7776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8f15a636469944ddb56489a74a75591b.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science (New York, N.Y.)", "issn": "1095-9203", "volume": "380", "issue": "6643", "pages": "eabn5856", "issn-l": "0036-8075"}, "abstract": "Species persistence can be influenced by the amount, type, and distribution of diversity across the genome, suggesting a potential relationship between historical demography and resilience. In this study, we surveyed genetic variation across single genomes of 240 mammals that compose the Zoonomia alignment to evaluate how historical effective population size (Ne) affects heterozygosity and deleterious genetic load and how these factors may contribute to extinction risk. We find that species with smaller historical Ne carry a proportionally larger burden of deleterious alleles owing to long-term accumulation and fixation of genetic load and have a higher risk of extinction. This suggests that historical demography can inform contemporary resilience. Models that included genomic data were predictive of species' conservation status, suggesting that, in the absence of adequate census or ecological data, genomic information may provide an initial risk assessment.", "doi": "10.1126/science.abn5856", "pmid": "37104572", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1893031"}, {"db": "pmc", "key": "PMC10184782"}], "notes": [], "created": "2026-09-23T07:40:18.022Z", "modified": "2026-09-23T07:40:18.317Z"}, {"entity": "publication", "iuid": "81174e492b9944f0bc162a8e44ad60e1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/81174e492b9944f0bc162a8e44ad60e1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/81174e492b9944f0bc162a8e44ad60e1"}}, "title": "Relating enhancer genetic variation across mammals to complex phenotypes using machine learning.", "authors": [{"family": "Kaplow", "given": "Irene M", "initials": "IM", "orcid": "0000-0002-8924-8269", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4fc8b6ee363a4ccaaea909392715888a.json"}}, {"family": "Lawler", "given": "Alyssa J", "initials": "AJ", "orcid": "0000-0002-2151-5164", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb3c0a5c01064277918e610c2e6f97d7.json"}}, {"family": "Sch\u00e4ffer", "given": "Daniel E", "initials": "DE", "orcid": "0000-0003-3608-152X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b7f399939ae14daa8c0bd9bf5b92a896.json"}}, {"family": "Srinivasan", "given": "Chaitanya", "initials": "C", "orcid": "0000-0002-1487-541X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/986e7c06dd8a401b8e27767519298c8e.json"}}, {"family": "Sestili", "given": "Heather H", "initials": "HH", "orcid": "0000-0002-3944-3429", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e39c7cd75c954a2d86175e7d4baa85c9.json"}}, {"family": "Wirthlin", "given": "Morgan E", "initials": "ME", "orcid": "0000-0001-7967-7070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7b1757207aa24108859d7c116bda19b7.json"}}, {"family": "Phan", "given": "BaDoi N", "initials": "BN", "orcid": "0000-0001-6331-5980", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2ba10919dc8445f9bf68539551f47c17.json"}}, {"family": "Prasad", "given": "Kavya", "initials": "K", "orcid": "0000-0003-3419-5670", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9bff88dfefa8411f8868fece7d412acb.json"}}, {"family": "Brown", "given": "Ashley R", "initials": "AR", "orcid": "0000-0002-3091-3930", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/74b99a2a10ea4d4c995e6fd3fff65fe6.json"}}, {"family": "Zhang", "given": "Xiaomeng", "initials": "X", "orcid": "0000-0002-8536-6460", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f3ed76faa8544096b5507e5beb1d29eb.json"}}, {"family": "Foley", "given": "Kathleen", "initials": "K", "orcid": "0000-0003-0923-1326", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/907a734d325d4f76bf083c68202f2e05.json"}}, {"family": "Genereux", "given": "Diane P", "initials": "DP", "orcid": "0000-0001-5770-0989", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/352ee25047c544aaa486a69e7e3333fc.json"}}, {"family": "Zoonomia Consortium**", "given": "", "initials": ""}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/612a779b69494f1ca9b6c5f1d84fd711.json"}}, {"family": "Meyer", "given": "Wynn K", "initials": "WK", "orcid": "0000-0001-7978-3877", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b1fba9de46a4c8c8cbbbec685a9b94c.json"}}, {"family": "Pfenning", "given": "Andreas R", "initials": "AR", "orcid": "0000-0002-3447-9801", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f7c2be6e32147d19f03c7ff88fb3f80.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science (New York, N.Y.)", "issn": "1095-9203", "volume": "380", "issue": "6643", "pages": "eabm7993", "issn-l": "0036-8075"}, "abstract": "Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent and functionally conserved despite low sequence conservation. We developed the Tissue-Aware Conservation Inference Toolkit (TACIT) to associate candidate enhancers with species' phenotypes using predictions from machine learning models trained on specific tissues. Applying TACIT to associate motor cortex and parvalbumin-positive interneuron enhancers with neurological phenotypes revealed dozens of enhancer-phenotype associations, including brain size-associated enhancers that interact with genes implicated in microcephaly or macrocephaly. TACIT provides a foundation for identifying enhancers associated with the evolution of any convergently evolved phenotype in any large group of species with aligned genomes.", "doi": "10.1126/science.abm7993", "pmid": "37104615", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1897368"}, {"db": "pmc", "key": "PMC10322212"}], "notes": [], "created": "2026-09-23T07:46:28.562Z", "modified": "2026-09-23T07:46:28.868Z"}]}