The genomic history and global expansion of domestic donkeys

Todd, Evelyn T.; Tonasso-Calvière, Laure; Chauvey, Loreleï; Schiavinato, Stéphanie; Fages, Antoine; Seguin-Orlando, Andaine; Clavel, Pierre; Khan, Naveed; Pérez‐Pardal, L.; Rosa, Laura Patterson; Librado, Pablo; Ringbauer, Harald; Verdugo, Marta Pereira; Southon, John; Aury, Jean‐Marc; Perdereau, Aude; Vila, Emmanuelle; Marzullo, Matilde; Prato, Ornella; Tecchiati, Umberto; Gianni, Giovanna Bagnasco; Tagliacozzo, Antonio; Tiné, Vincenzo; Alhaique, Francesca; Cardoso, João Luís; Valente, Maria João; Antunes, Miguel Telles; Frantz, Laurent; Shapiro, Beth; Bradley, Daniel G.; Boulbes, Nicolas; Gardeisen, Armelle; Horwitz, Liora Kolska; Öztan, Aliye; Arbuckle, Benjamin S.; Onar, Vedat; Clavel, Benoît; Lepetz, Sébastien; Vahdati, Ali A.; Davoudi, Hossein; Karimlu, Azadeh Fatemeh Mohaseb; Mashkour, Marjan; Bouchez, Olivier; Donnadieu, Cécile; Wincker, Patrick; Brooks, Samantha A.; Beja‐Pereira, Albano; Wu, Dong‐Dong; Orlando, Ludovic

doi:10.1126/science.abo3503

Cited by 21 publications

(15 citation statements)

References 102 publications

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“…6A). Many of these populations retain genetic diversity lost from their native conspecific populations ( 14 , 49 , 50 ) and thus, genetically, may be a lifeline to the persistence of these species globally. Moreover, active conservation efforts in the native ranges of some of these species is difficult, if not impossible; for example, the remaining 23-200 African wild asses occur in areas currently occupied by warring groups ( 10 ).…”

Section: Discussionmentioning

confidence: 99%

Preventing extinction in an age of species migration and planetary change

Lundgren,

Wallach,

Svenning

et al. 2023

Preprint

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International and national conservation policies almost exclusively focus on conserving species in their historic native ranges, thus excluding species that have dispersed on their own accord or have been introduced by people. Given that many of these "migrant" species are threatened in their native ranges, conservation goals that explicitly exclude these migrant populations may overlook opportunities to prevent extinctions and respond dynamically to rapidly changing environmental and climatic conditions. Focusing on terrestrial mammals, we quantified the extent to which migration, in this case via introductions, has provided new homes for threatened mammal species. We then devised alternative scenarios for the inclusion of migrant populations in mainstream conservation policy with the aim of preventing global species extinctions and used spatial prioritization algorithms to simulate how these scenarios could change global spatial conservation priorities. We found that 22% of all identified migrant mammals (70 species) are threatened in their native ranges, mirroring the 25% of all mammals that are threatened. Reassessing global threat statuses by combining native and migrant ranges reduced the threat status of 23 species (~33% of threatened migrants). Thus, including migrant populations in threat assessments provides a more accurate assessment of actual global extinction risk among species. Spatial prioritization simulations showed that reimagining the role of migrant populations to prevent global species extinction could increase the importance of overlooked landscapes, particularly in central Australia. Our results indicate that these various and non-exhaustive ways to consider migrant populations, with due consideration for potential conservation conflicts with resident taxa, may provide unprecedented opportunities to prevent species extinctions. We present these alternatives and spatial simulations to stimulate discussion on how conservation ought to respond, both pragmatically and ethically, to rapid environmental change in order to best prevent extinctions.

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Section: Discussionmentioning

confidence: 99%

Preventing extinction in an age of species migration and planetary change

Lundgren,

Wallach,

Svenning

et al. 2023

Preprint

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“…2016; Librado et al . 2021; Todd et al . 2022) and the domestication process, according to archeological records, started around 10,000 years ago (Ahmad et al .…”

Section: Methodsmentioning

confidence: 99%

Detection of Domestication Signals through the Analysis of the Full Distribution of Fitness Effects using Simulations

Vourlaki

Castellano

Gutenkunst

et al. 2022

Preprint

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As a consequence of the process of domestication, wild and domestic individuals are adapted to very different environmental conditions. Although the phenotypic consequences of domestication are observable, the genetic causes are not evident in many cases. Artificial selection could be modifying the selection coefficients of new and standing variation in the population under domestication. Here, we aim to detect a genome-wide signal of domestication under a model of polygenic adaptation. We use forward simulations to investigate the 1D and 2D site frequency spectra (SFS) of mutations in two populations (Wild and Domestic) with divergent histories (demographic and selective) following a domestication split. We simulate ten different scenarios, varying the strength of selection upon beneficial mutations and the proportion of mutations whose selection coefficients change after domestication. First, we describe that in domesticated populations selection at linked sites needs to be invoked to explain the SFS of neutral mutations and that the mode of linked selection affecting the neutral SFS depends on the duration of the domestication bottleneck. Second, we find that some aspects of the full distribution of fitness effects (DFE), such as the shape and strength of the deleterious DFE, are accurately estimated in both populations when using only the 1D-SFS. However, the detection of significant differences in the beneficial DFE between populations remains challenging in most, but not all simulated scenarios when only the 1D-SFS is used. Third, when considering the 2D-SFS and a new joint DFE model, we are able to detect more subtle differences in the full DFE that are hidden in the 1D-SFS analysis. In conclusion, our work highlights the strengths and limitations of detecting a polygenic signal of domestication under a variety of domestication scenarios and genetic architectures.

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“…The data analysed in this study was obtained from the following archive study accessions: PRJEB54831 (ENA) 8 , PRJEB51180 (ENA) 9 , PRJCA005576 (GSA) 10 , PRJEB52849 (ENA) 11 , PRJEB42656 (ENA) 12 , PRJEB52230 (ENA) 13 , PRJNA786530 (SRA) 14 , PRJNA1005336 (SRA) 15 , PRJEB51440 (ENA) 16 , PRJEB56773 (ENA) 17 , PRJEB49291 (ENA) 18 , PRJEB42781 (ENA) 19 , PRJEB46734 (ENA) 20 , PRJNA798381 (SRA) 21 , PRJEB42269 (ENA) 22 , PRJEB47891 (ENA) 23 , PRJEB54899 (ENA) 24 , PRJEB43715 (ENA) 25 , PRJEB39134 (ENA) 26 , PRJEB46162 (ENA) 27 , PRJEB46875 (ENA) 28 , PRJEB44430 (ENA) 29 , PRJEB42199 (ENA) 30 , PRJEB38555 (ENA) 31 , PRJEB55327 (ENA) 32 , PRJEB56213 (ENA) 33 , PRJEB51862 (ENA) 34 , PRJEB58698 (ENA) 35 , PRJEB62503 (ENA) 36 , PRJEB66319 (ENA) 37 , PRJEB59008 (ENA) 38 , PRJEB61818 (ENA) 39 , PRJEB50368 (ENA) 40 , PRJEB50857 (ENA) 41 , PRJCA003870 (GSA) 42 , PRJCA003699 (GSA) 43 , PRJEB53475 (ENA) 44 , PRJEB37782 (ENA) 45 , PRJNA687817 (SRA) 46 , PRJEB42372 (ENA) 47 , PRJEB66422 (ENA) 48 , PRJEB57364 (ENA) 49 .…”

Section: Data Availabilitymentioning

confidence: 99%

Improving data archiving practices in ancient genomics

Bergström

2023

Preprint

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The sequencing of ancient DNA from preserved biological remains is producing a rich record of past genetic diversity in humans and other species. However, unless the primary data is made available in public archives in an appropriate fashion, its long-term value will not be fully realised. I surveyed publicly archived data from 28 recent ancient genomics studies. I found that half of the studies archived incomplete subsets of the generated genomic data, preventing accurate replication and representing a loss of data of potential use for future research. None of the studies met all archiving criteria that could be considered best practice. Based on these results, I make six recommendations for data producers: 1) archive all sequencing reads, not just those that can be aligned to a reference genome, 2) archive read alignments as well, but as secondary analysis files linked to the underlying raw read files, 3) provide correct experiment metadata on how samples, libraries and sequencing runs relate to each other, 4) provide informative sample metadata in the public archives, 5) publish and archive data from screening, low-coverage, poorly performing and negative experiments, and 6) review data archiving as part of peer review processes. Given the reliance on destructive sampling of finite material, I argue that ancient genomics studies have a particularly strong responsibility to ensure the longevity and reusability of generated data.

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The genomic history and global expansion of domestic donkeys

Cited by 21 publications

References 102 publications

Preventing extinction in an age of species migration and planetary change

Preventing extinction in an age of species migration and planetary change

Detection of Domestication Signals through the Analysis of the Full Distribution of Fitness Effects using Simulations

Improving data archiving practices in ancient genomics

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