Genetic signatures of lineage fusion closely resemble population decline
Abstract Accurate interpretation of the genetic signatures of past demographic events is crucial for reconstructing evolutionary history. Lineage fusion (complete merging, resulting in a single panmictic population) is a special case of secondary contact that is seldom considered. Here, the circumst...
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| Format: | Article |
| Language: | English |
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Wiley
2023-11-01
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| Series: | Ecology and Evolution |
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| Online Access: | https://doi.org/10.1002/ece3.10725 |
| _version_ | 1797448654785609728 |
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| author | Ryan C. Garrick |
| author_facet | Ryan C. Garrick |
| author_sort | Ryan C. Garrick |
| collection | DOAJ |
| description | Abstract Accurate interpretation of the genetic signatures of past demographic events is crucial for reconstructing evolutionary history. Lineage fusion (complete merging, resulting in a single panmictic population) is a special case of secondary contact that is seldom considered. Here, the circumstances under which lineage fusion can be distinguished from population size constancy, growth, bottleneck, and decline were investigated. Multi‐locus haplotype data were simulated under models of lineage fusion with different divergence versus sampling lag times (D:L ratios). These pseudo‐observed datasets also differed in their allocation of a fixed amount of sequencing resources (number of sampled alleles, haplotype length, number of loci). Distinguishability of lineage fusion versus each of 10 untrue non‐fusion scenarios was quantified based on six summary statistics (neutrality tests). Some datasets were also analyzed using extended Bayesian skyline plots. Results showed that signatures of lineage fusion very closely resemble those of decline—high distinguishability was generally limited to the most favorable scenario (D:L = 9), using the most sensitive summary statistics (FS and ZnS), coupled with the optimal sequencing resource allocation (maximizing number of loci). Also, extended Bayesian skyline plots often erroneously inferred population decline. Awareness of the potential for lineage fusion to carry the hallmarks of population decline is critical. |
| first_indexed | 2024-03-09T14:13:31Z |
| format | Article |
| id | doaj.art-3120eb2946d24a549b361a693eb7874f |
| institution | Directory Open Access Journal |
| issn | 2045-7758 |
| language | English |
| last_indexed | 2024-03-09T14:13:31Z |
| publishDate | 2023-11-01 |
| publisher | Wiley |
| record_format | Article |
| series | Ecology and Evolution |
| spelling | doaj.art-3120eb2946d24a549b361a693eb7874f2023-11-29T05:44:08ZengWileyEcology and Evolution2045-77582023-11-011311n/an/a10.1002/ece3.10725Genetic signatures of lineage fusion closely resemble population declineRyan C. Garrick0Department of Biology University of Mississippi Oxford Mississippi USAAbstract Accurate interpretation of the genetic signatures of past demographic events is crucial for reconstructing evolutionary history. Lineage fusion (complete merging, resulting in a single panmictic population) is a special case of secondary contact that is seldom considered. Here, the circumstances under which lineage fusion can be distinguished from population size constancy, growth, bottleneck, and decline were investigated. Multi‐locus haplotype data were simulated under models of lineage fusion with different divergence versus sampling lag times (D:L ratios). These pseudo‐observed datasets also differed in their allocation of a fixed amount of sequencing resources (number of sampled alleles, haplotype length, number of loci). Distinguishability of lineage fusion versus each of 10 untrue non‐fusion scenarios was quantified based on six summary statistics (neutrality tests). Some datasets were also analyzed using extended Bayesian skyline plots. Results showed that signatures of lineage fusion very closely resemble those of decline—high distinguishability was generally limited to the most favorable scenario (D:L = 9), using the most sensitive summary statistics (FS and ZnS), coupled with the optimal sequencing resource allocation (maximizing number of loci). Also, extended Bayesian skyline plots often erroneously inferred population decline. Awareness of the potential for lineage fusion to carry the hallmarks of population decline is critical.https://doi.org/10.1002/ece3.10725Bayesian skyline plotdemographic historyfission‐fusionneutrality testphylogeographypopulation merging |
| spellingShingle | Ryan C. Garrick Genetic signatures of lineage fusion closely resemble population decline Ecology and Evolution Bayesian skyline plot demographic history fission‐fusion neutrality test phylogeography population merging |
| title | Genetic signatures of lineage fusion closely resemble population decline |
| title_full | Genetic signatures of lineage fusion closely resemble population decline |
| title_fullStr | Genetic signatures of lineage fusion closely resemble population decline |
| title_full_unstemmed | Genetic signatures of lineage fusion closely resemble population decline |
| title_short | Genetic signatures of lineage fusion closely resemble population decline |
| title_sort | genetic signatures of lineage fusion closely resemble population decline |
| topic | Bayesian skyline plot demographic history fission‐fusion neutrality test phylogeography population merging |
| url | https://doi.org/10.1002/ece3.10725 |
| work_keys_str_mv | AT ryancgarrick geneticsignaturesoflineagefusioncloselyresemblepopulationdecline |