{"doi":"10.1093/g3journal/jkae153","title":"ONeSAMP 3.0: estimation of effective population size via single nucleotide polymorphism data from one population","abstract":"The genetic effective size (Ne) is arguably one of the most important characteristics of a population as it impacts the rate of loss of genetic diversity. Methods that estimate Ne are important in population and conservation genetic studies as they quantify the risk of a population being inbred or lacking genetic diversity. Yet there are very few methods that can estimate the Ne from data from a single population and without extensive information about the genetics of the population, such as a linkage map, or a reference genome of the species of interest. We present ONeSAMP 3.0, an algorithm for estimating Ne from single nucleotide polymorphism data collected from a single population sample using approximate Bayesian computation and local linear regression. We demonstrate the utility of this approach using simulated Wright-Fisher populations, and empirical data from five endangered Channel Island fox (Urocyon littoralis) populations to evaluate the performance of ONeSAMP 3.0 compared to a commonly used Ne estimator. Our results show that ONeSAMP 3.0 is broadly applicable to natural populations and is flexible enough that future versions could easily include summary statistics appropriate for a suite of biological and sampling conditions. ONeSAMP 3.0 is publicly available under the GNU General Public License at https://github.com/AaronHong1024/ONeSAMP_3.","journal":"G3 Genes Genomes Genetics","year":2024,"id":463001,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":7,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9186,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":19194,"name":"Rebecca G. Cheek","orcid":"0000-0002-7935-3153","position":1,"is_corresponding":false},{"id":1293608,"name":"Suhashi Nihara De Silva","orcid":null,"position":2,"is_corresponding":false},{"id":321618,"name":"Kingshuk Mukherjee","orcid":"0000-0002-1647-8741","position":3,"is_corresponding":false},{"id":1293609,"name":"Isha Yooseph","orcid":null,"position":4,"is_corresponding":false},{"id":496290,"name":"Marco Antônio Oliva","orcid":"0000-0003-0525-3114","position":5,"is_corresponding":false},{"id":1293610,"name":"Mark Heim","orcid":null,"position":6,"is_corresponding":false},{"id":19199,"name":"W. Chris Funk","orcid":"0000-0002-6466-3618","position":7,"is_corresponding":false},{"id":617006,"name":"David A. Tallmon","orcid":null,"position":8,"is_corresponding":false},{"id":23991,"name":"Christina Boucher","orcid":"0000-0001-9509-9725","position":9,"is_corresponding":false},{"id":1186071,"name":"Aaron Hong","orcid":"0000-0002-1361-7216","position":0,"is_corresponding":true}],"reference_count":55,"raw_metadata":null,"created_at":"2026-07-19T02:04:28.838123Z","pmid":"38996058","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}