Genomes from historical Drosophila melanogaster specimens illuminate adaptive and demographic changes across more than 200 years of evolution
Shpak, Max ; Ghanavi, Hamid R LU
; Lange, Jeremy D
; Pool, John E
and Stensmyr, Marcus C
LU
(2023)
In PLoS Biology
21(10).
- Abstract
The ability to perform genomic sequencing on long-dead organisms is opening new frontiers in evolutionary research. These opportunities are especially notable in the case of museum collections, from which countless documented specimens may now be suitable for genomic analysis-if data of sufficient quality can be obtained. Here, we report 25 newly sequenced genomes from museum specimens of the model organism Drosophila melanogaster, including the oldest extant specimens of this species. By comparing historical samples ranging from the early 1800s to 1933 against modern-day genomes, we document evolution across thousands of generations, including time periods that encompass the species' initial occupation of northern Europe and an era of... (More)
The ability to perform genomic sequencing on long-dead organisms is opening new frontiers in evolutionary research. These opportunities are especially notable in the case of museum collections, from which countless documented specimens may now be suitable for genomic analysis-if data of sufficient quality can be obtained. Here, we report 25 newly sequenced genomes from museum specimens of the model organism Drosophila melanogaster, including the oldest extant specimens of this species. By comparing historical samples ranging from the early 1800s to 1933 against modern-day genomes, we document evolution across thousands of generations, including time periods that encompass the species' initial occupation of northern Europe and an era of rapidly increasing human activity. We also find that the Lund, Sweden population underwent local genetic differentiation during the early 1800s to 1933 interval (potentially due to drift in a small population) but then became more similar to other European populations thereafter (potentially due to increased migration). Within each century-scale time period, our temporal sampling allows us to document compelling candidates for recent natural selection. In some cases, we gain insights regarding previously implicated selection candidates, such as ChKov1, for which our inferred timing of selection favors the hypothesis of antiviral resistance over insecticide resistance. Other candidates are novel, such as the circadian-related gene Ahcy, which yields a selection signal that rivals that of the DDT resistance gene Cyp6g1. These insights deepen our understanding of recent evolution in a model system, and highlight the potential of future museomic studies.
(Less)
- author
- Shpak, Max
; Ghanavi, Hamid R
LU
; Lange, Jeremy D
; Pool, John E
and Stensmyr, Marcus C
LU
- organization
- publishing date
- 2023-10
- type
- Contribution to journal
- publication status
- published
- subject
- in
- PLoS Biology
- volume
- 21
- issue
- 10
- article number
- e3002333
- pages
- 31 pages
- publisher
- Public Library of Science (PLoS)
- external identifiers
-
- scopus:85174305922
- pmid:37824452
- ISSN
- 1545-7885
- DOI
- 10.1371/journal.pbio.3002333
- project
- The Max Planck Center on next Generation Insect Chemical Ecology
- language
- English
- LU publication?
- yes
- additional info
- Copyright: © 2023 Shpak et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
- id
- 6a33911a-80f3-43e8-8725-ad5cc98dbc0b
- date added to LUP
- 2023-10-17 00:12:43
- date last changed
- 2024-04-14 05:40:08
@article{6a33911a-80f3-43e8-8725-ad5cc98dbc0b,
abstract = {{<p>The ability to perform genomic sequencing on long-dead organisms is opening new frontiers in evolutionary research. These opportunities are especially notable in the case of museum collections, from which countless documented specimens may now be suitable for genomic analysis-if data of sufficient quality can be obtained. Here, we report 25 newly sequenced genomes from museum specimens of the model organism Drosophila melanogaster, including the oldest extant specimens of this species. By comparing historical samples ranging from the early 1800s to 1933 against modern-day genomes, we document evolution across thousands of generations, including time periods that encompass the species' initial occupation of northern Europe and an era of rapidly increasing human activity. We also find that the Lund, Sweden population underwent local genetic differentiation during the early 1800s to 1933 interval (potentially due to drift in a small population) but then became more similar to other European populations thereafter (potentially due to increased migration). Within each century-scale time period, our temporal sampling allows us to document compelling candidates for recent natural selection. In some cases, we gain insights regarding previously implicated selection candidates, such as ChKov1, for which our inferred timing of selection favors the hypothesis of antiviral resistance over insecticide resistance. Other candidates are novel, such as the circadian-related gene Ahcy, which yields a selection signal that rivals that of the DDT resistance gene Cyp6g1. These insights deepen our understanding of recent evolution in a model system, and highlight the potential of future museomic studies.</p>}},
author = {{Shpak, Max and Ghanavi, Hamid R and Lange, Jeremy D and Pool, John E and Stensmyr, Marcus C}},
issn = {{1545-7885}},
language = {{eng}},
number = {{10}},
publisher = {{Public Library of Science (PLoS)}},
series = {{PLoS Biology}},
title = {{Genomes from historical Drosophila melanogaster specimens illuminate adaptive and demographic changes across more than 200 years of evolution}},
url = {{http://dx.doi.org/10.1371/journal.pbio.3002333}},
doi = {{10.1371/journal.pbio.3002333}},
volume = {{21}},
year = {{2023}},
}