Evolutionary History, Genomic Adaptation to Toxic Diet, and Extinction of the Carolina Parakeet

Gelabert, Pere; Sandoval-Velasco, Marcela; Serres, Aitor; Manuel, Marc de; Renom, Pere; Margaryan, Ashot; Stiller, Josefin; de-Dios, Toni; Fang, Qi; Feng, Shaohong; Mañosa, Santi; Pacheco, George; Ferrando-Bernal, Manuel; Shi, Guolin; Hao, Fei; Chen, Xianqing; Petersen, Bent; Olsen, Remi André; Navarro, Arcadi; Deng, Yuan; Dalén, Love; Marquès-Bonet, Tomàs; Zhang, Guojie; Antunes, Agostinho; Gilbert, M. Thomas P.; Lalueza‐Fox, Carles

doi:10.1016/j.cub.2019.10.066

Cited by 26 publications

(30 citation statements)

References 68 publications

(56 reference statements)

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“…Overall, our dataset establishes birds as a system with unparalleled genomic resources. The B10K consortium is using these genomes and alignments to reconstruct the evolutionary history of birds, and the genomic patterns that underlie the diversity of avian phenotypes 34,35 . The genomes will further serve the community in two ways.…”

Section: Dense Sampling Of Bird Diversity Increases Power Of Comparatmentioning

confidence: 99%

Dense sampling of bird diversity increases power of comparative genomics

Feng

Stiller

Deng

et al. 2020

Nature

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Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.

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Section: Dense Sampling Of Bird Diversity Increases Power Of Comparatmentioning

confidence: 99%

Dense sampling of bird diversity increases power of comparative genomics

Feng

Stiller

Deng

et al. 2020

Nature

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309

317

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“…Therefore, even slow rates of persecution may have caused long‐term population declines and range contractions of several species, increasing their risk of extinction. In fact, it was argued that the blue‐winged macaw ( Primolius maracana ), once considered as crop pest, became extinct in Argentina just after five decades of persecution by farmers (Bodrati et al., 2006) and that hunting by farmers contributed to the abrupt global extinction of the Carolina parakeet ( Conuropsis carolinensis ) in North America (Gelabert et al., 2020).…”

Section: Discussionmentioning

confidence: 99%

When does agriculture enter into conflict with wildlife? A global assessment of parrot–agriculture conflicts and their conservation effects

Barbosa

Hiraldo

Romero

et al. 2020

Diversity and Distributions

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Aim: No human activity has changed natural habitat availability and ecosystem functioning more than agriculture. As a consequence, species may be forced to use croplands as foraging habitat, resulting in potential conflicts with farmers. To assess the causes and consequences of wildlife-agriculture interactions, we investigated the underlying associations among species traits, climate and landscapes factors that determine parrot species to use croplands, and related them to their conservation status. Location: Global. Methods: We used parrots as a model due to their global distribution, high behavioural plasticity, high proportion of species using croplands (43%) and threatened species (26%). Within the distribution range of the 398 extant parrot species, we calculated annual averages and seasonality of ecosystem productivity, climate conditions and land-use patterns from satellite data. We then categorized species conservation status using information provided by IUCN. Results: We found that habitat degradation, where biodiversity is low and primary productivity is low and intermittent, together with the plasticity of species to use different habitats, is key interrelated conditions that increase the likelihood of species to use croplands worldwide. The persecution of parrots as crop pests varied among regions, being higher for large-bodied species, those with small distributions, and in highly human-impacted areas. Moreover, persecution is contributing to the global population decline and extinction risk of parrots, especially in those species with small distribution ranges. Main conclusions: Parrot-agriculture conflicts may affect both the conservation of parrot species and their key ecological functions. Our results highlight the importance of using multi-specific and multi-source information to understand and predict where and why human-wildlife conflicts may arise, as their main drivers interact and are heterogeneous at large spatial scales. Further studies should evaluate the actual extent and economic impact of crop losses caused by wild species to help solve agriculture-wildlife conflicts. | 5 BARBOSA et Al.

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“…Genomic and epi-genomic analyses using museum specimens could be used to elucidate the mechanisms behind these problems, as temporal difference can be detected using present and past samples. Gelabert et al (2020) and Irestedt et al (2019) determined the whole genomes of extinct species and discussed their processes of extinction on the basis of whole genome data. Moreover, Rubi, Knowles, and Dantzer (2020) demonstrated the utility of museum specimens for conducting epi-genomic analyses.…”

Section: Contributions Of Museum Specimens To Conservation Geneticsmentioning

confidence: 99%

“…In the future, new low-cost and time-efficient analysis methods could also be developed. Second, utilizing genomic information is useful for understanding the temporal transition of mutations or methylations of functional genes (Gelabert et al, 2020;Irestedt et al, 2019;Rubi et al, 2020). This knowledge is also important for informing the conservation of endangered species.…”

Section: Conclusion and Perspectives For Future Usementioning

confidence: 99%

Museum specimens: An overlooked and valuable material for conservation genetics

Nakahama

2020

Ecological Research

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Museum specimens include genetic information from when they were collected. This historical information, which is very difficult to ascertain from samples collected currently, could be a valuable material for use in conservation genetics. However, the genetic analysis of museum specimens is technically difficult because of DNA fragmentation and the deamination of cytosine to uracil. In recent years, various methods have been developed for the genetic analysis of museum specimens, such as data analysis techniques including next-generation sequencing. The development of approaches that extract historical genetic information from museum specimens is expected to provide a new perspective on conservation genetics. This review focuses on the availability of museum specimens as genetic resources for conservation genetics. Some case studies are introduced, and perspectives on the future utility of conservation genetic studies using museum specimens are discussed. Moreover, recommended genetic analysis methods and important points for the usage of museum specimens are presented. This review provides a strong case for increasing the usage of museum specimens in conservation genetics studies in the future.

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Evolutionary History, Genomic Adaptation to Toxic Diet, and Extinction of the Carolina Parakeet

Cited by 26 publications

References 68 publications

Dense sampling of bird diversity increases power of comparative genomics

Dense sampling of bird diversity increases power of comparative genomics

When does agriculture enter into conflict with wildlife? A global assessment of parrot–agriculture conflicts and their conservation effects

Museum specimens: An overlooked and valuable material for conservation genetics

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