An ‛Aukward’ Tale: A Genetic Approach to Discover the Whereabouts of the Last Great Auks
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Information
2.2. DNA Extraction
2.3. Data Generation
2.4. Read Processing
3. Results
4. Discussion
5. Conclusions
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Lab ID | Bird Name, Number & Description | Origin & Date | Institution | Curator/Collector | Institution Number | Sample Type/Sampling Method |
---|---|---|---|---|---|---|
MK131 | Last Great Auk 1 Oesophagus (male) | Eldey Island, Iceland. Date: June 1844 | Natural History Museum of Denmark. Copenhagen, Denmark | J. Fjeldså/ J. Thomas | NHMD 153069 | Oesophagus. Tissue cut from end of oesophagus. |
MK132 | Last Great Auk 2 Oesophagus (female) | Eldey Island, Iceland. Date: June 1844 | Natural History Museum of Denmark. Copenhagen, Denmark | J. Fjeldså/ J. Thomas | NHMD 153070 | Oesophagus. Tissue cut from end of oesophagus. |
MK133 | The Oldenburg Auk Fuller: Bird no. 47, Grieve: no. 57, Hahn: no. 77 Adult in summer plumage | Iceland. Probably Eldey. Date: Unknown | Landesmuseum Natur und Mensch Oldenburg. Germany | C. Barilaro | AVE 8086 | Body tissue. Tissue cut from body of bird under wing. |
MK134 | The Bremen Auk Fuller: Bird no. 36, Grieve: no. 10, Hahn: no. 71 Adult in summer plumage | Unknown. Probably Eldey. Date: Unknown | Übersee-Museum Bremen. Germany | M. Stiller | RKNr. 2392 | Toepad tissue. Tissue cut from feet. |
MK135 | The Brussels Auk Fuller: Bird no. 3, Grieve: no. 15, Hahn: no. 6 Adult in summer plumage | Probably Eldey Date: Unknown perhaps June, 1844 | Institut Royal des Sciences Naturelles de Belgique. Brussels, Belgium | G. Lenglet | RBINS 5355 | Toepad tissue. Tissue cut from feet |
MK136 | Dawson Rowley’s Los Angeles Auk Fuller: Bird no. 73, Grieve no. 13, Hahn: no. 5 Adult in summer plumage, said to be female | Iceland. Probably Eldey. Date: Unknown perhaps June, 1844 | Natural History Museum of Los Angeles County. USA | K. Garett | LACM 76476 | Feather. Feathers plucked from body of bird. |
MK138 | The Schleswig-Holstein Auk Fuller: Bird no. 42, Grieve: no. 31, Hahn: no. 74 Adult in summer plumage | Unknown Date: Unknown | Zoologisches Museum der Christian-Albrechts Universität zu Kiel. Germany | D. Brandis/ L. Rosotta | cat. No. A0585 | Toepad tissue. Tissue cut from feet. |
LastGA2_Heart | Last Great Auk 2 Heart (female) | Eldey Island, Iceland. Date: June 1844 | Natural History Museum of Denmark. Copenhagen, Denmark | J. Fjeldså/ J. Haile | NHMD 153070 | Heart. Tissue cut from aorta. |
Sample | GenBank Accession Number | Number of Reads | Number of Unique Reads Mapping to Reference Mitogenome | Estimated Coverage from Unique Hits | Relaxed Settings Sequence Length (bp 1) | Strict Settings Sequence Length (bp) |
---|---|---|---|---|---|---|
MK131 | MF188883 | 300754 (read pairs) | 30,297 | 74.40 | 16,001 | 15,067 |
MK132 | NA | 550631 (read pairs) | 2366 | 6.23 | 13,267 | 3312 |
MK133 | MF188884 | 429392 (read pairs) | 8750 | 23.04 | 16,251 | 14,240 |
MK134 | MF188885 | 343766 (read pairs) | 86,325 | 288.62 | 16,607 | 16,526 |
MK135 | MF188886 | 579992 (read pairs) | 27,767 | 88.90 | 16,554 | 16,356 |
MK136 | MF188887 | 563635 (read pairs) | 24,401 | 67.83 | 16,330 | 15,833 |
MK138 | MF188888 | 10796460 (SE 2 reads) | 2799 | 9.76 | 16509 | 7866 |
LastGA2_Heart | MF188889 | 957970612 (SE reads) | 121,886 | 430.09 | 16,698 | 16,649 |
MK131 | MK133 | MK134 | MK135 | MK136 | MK138 | LastGA2_Heart | |
---|---|---|---|---|---|---|---|
MK131_LastGA1 | |||||||
MK133_Oldenburg | 17 | ||||||
MK134_Bremen | 18 | 23 | |||||
MK135_Brussels | 0 | 17 | 18 | ||||
MK136_LA | 16 | 23 | 20 | 16 | |||
MK138_Kiel | 14 | 11 | 20 | 14 | 20 | ||
LastGA2_Heart | 16 | 23 | 20 | 16 | 18 | 20 |
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Thomas, J.E.; Carvalho, G.R.; Haile, J.; Martin, M.D.; Castruita, J.A.S.; Niemann, J.; Sinding, M.-H.S.; Sandoval-Velasco, M.; Rawlence, N.J.; Fuller, E.; et al. An ‛Aukward’ Tale: A Genetic Approach to Discover the Whereabouts of the Last Great Auks. Genes 2017, 8, 164. https://doi.org/10.3390/genes8060164
Thomas JE, Carvalho GR, Haile J, Martin MD, Castruita JAS, Niemann J, Sinding M-HS, Sandoval-Velasco M, Rawlence NJ, Fuller E, et al. An ‛Aukward’ Tale: A Genetic Approach to Discover the Whereabouts of the Last Great Auks. Genes. 2017; 8(6):164. https://doi.org/10.3390/genes8060164
Chicago/Turabian StyleThomas, Jessica E., Gary R. Carvalho, James Haile, Michael D. Martin, Jose A. Samaniego Castruita, Jonas Niemann, Mikkel-Holger S. Sinding, Marcela Sandoval-Velasco, Nicolas J. Rawlence, Errol Fuller, and et al. 2017. "An ‛Aukward’ Tale: A Genetic Approach to Discover the Whereabouts of the Last Great Auks" Genes 8, no. 6: 164. https://doi.org/10.3390/genes8060164
APA StyleThomas, J. E., Carvalho, G. R., Haile, J., Martin, M. D., Castruita, J. A. S., Niemann, J., Sinding, M. -H. S., Sandoval-Velasco, M., Rawlence, N. J., Fuller, E., Fjeldså, J., Hofreiter, M., Stewart, J. R., Gilbert, M. T. P., & Knapp, M. (2017). An ‛Aukward’ Tale: A Genetic Approach to Discover the Whereabouts of the Last Great Auks. Genes, 8(6), 164. https://doi.org/10.3390/genes8060164