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Buswell VG, Ellis JS, Huml JV, Wragg D, Barnett MW, Brown A, Knight ME. When One's Not Enough: Colony Pool-Seq Outperforms Individual-Based Methods for Assessing Introgression in Apis mellifera mellifera. INSECTS 2023; 14:insects14050421. [PMID: 37233049 DOI: 10.3390/insects14050421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023]
Abstract
The human management of honey bees (Apis mellifera) has resulted in the widespread introduction of subspecies outside of their native ranges. One well known example of this is Apis mellifera mellifera, native to Northern Europe, which has now been significantly introgressed by the introduction of C lineage honey bees. Introgression has consequences for species in terms of future adaptive potential and long-term viability. However, estimating introgression in colony-living haplodiploid species is challenging. Previous studies have estimated introgression using individual workers, individual drones, multiple drones, and pooled workers. Here, we compare introgression estimates via three genetic approaches: SNP array, individual RAD-seq, and pooled colony RAD-seq. We also compare two statistical approaches: a maximum likelihood cluster program (ADMIXTURE) and an incomplete lineage sorting model (ABBA BABA). Overall, individual approaches resulted in lower introgression estimates than pooled colonies when using ADMIXTURE. However, the pooled colony ABBA BABA approach resulted in generally lower introgression estimates than all three ADMIXTURE estimates. These results highlight that sometimes one individual is not enough to assess colony-level introgression, and future studies that do use colony pools should not be solely dependent on clustering programs for introgression estimates.
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Affiliation(s)
- Victoria G Buswell
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
- Information and Computational Sciences, The James Hutton Institute, Dundee DD2 5DA, UK
| | - Jonathan S Ellis
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
| | - J Vanessa Huml
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
| | - David Wragg
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
- Beebytes Analytics CIC, Roslin Innovation Centre, Easter Bush Campus, Roslin EH25 9RG, UK
| | - Mark W Barnett
- Beebytes Analytics CIC, Roslin Innovation Centre, Easter Bush Campus, Roslin EH25 9RG, UK
| | - Andrew Brown
- B4, Newton Farm Metherell, Cornwall, Callington PL17 8DQ, UK
| | - Mairi E Knight
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
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De Angelis F, Romboni M, Veltre V, Catalano P, Martínez-Labarga C, Gazzaniga V, Rickards O. First Glimpse into the Genomic Characterization of People from the Imperial Roman Community of Casal Bertone (Rome, First–Third Centuries AD). Genes (Basel) 2022; 13:genes13010136. [PMID: 35052476 PMCID: PMC8774527 DOI: 10.3390/genes13010136] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/04/2022] [Accepted: 01/08/2022] [Indexed: 02/01/2023] Open
Abstract
This paper aims to provide a first glimpse into the genomic characterization of individuals buried in Casal Bertone (Rome, first–third centuries AD) to gain preliminary insight into the genetic makeup of people who lived near a tannery workshop, fullonica. Therefore, we explored the genetic characteristics of individuals who were putatively recruited as fuller workers outside the Roman population. Moreover, we identified the microbial communities associated with humans to detect microbes associated with the unhealthy environment supposed for such a workshop. We examined five individuals from Casal Bertone for ancient DNA analysis through whole-genome sequencing via a shotgun approach. We conducted multiple investigations to unveil the genetic components featured in the samples studied and their associated microbial communities. We generated reliable whole-genome data for three samples surviving the quality controls. The individuals were descendants of people from North African and the Near East, two of the main foci for tannery and dyeing activity in the past. Our evaluation of the microbes associated with the skeletal samples showed microbes growing in soils with waste products used in the tannery process, indicating that people lived, died, and were buried around places where they worked. In that perspective, the results represent the first genomic characterization of fullers from the past. This analysis broadens our knowledge about the presence of multiple ancestries in Imperial Rome, marking a starting point for future data integration as part of interdisciplinary research on human mobility and the bio-cultural characteristics of people employed in dedicated workshops.
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Affiliation(s)
- Flavio De Angelis
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy; (V.V.); (C.M.-L.); (O.R.)
- Correspondence: ; Tel.: +39-0672594350
| | - Marco Romboni
- Department of Biology, University of Pisa, 56121 Pisa, Italy;
| | - Virginia Veltre
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy; (V.V.); (C.M.-L.); (O.R.)
- PhD Program in Evolutionary Biology and Ecology, Department of Biology, University of Rome Tor Vergata, 00133 Roma, Italy
| | - Paola Catalano
- Former Servizio di Antropologia, Soprintendenza Speciale Archeologia, Belle Arti e Paesaggio di Roma, 00185 Roma, Italy;
| | - Cristina Martínez-Labarga
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy; (V.V.); (C.M.-L.); (O.R.)
| | - Valentina Gazzaniga
- Unità di Storia della Medicina e Bioetica, Sapienza University of Rome, 00185 Roma, Italy;
| | - Olga Rickards
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy; (V.V.); (C.M.-L.); (O.R.)
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