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Genes along the Anthropocene: a two-scale study of the impacts of human-mediated perturbations on genetic variation in temperate species

Titel Englisch Genes along the Anthropocene: a two-scale study of the impacts of human-mediated perturbations on genetic variation in temperate species
Gesuchsteller/in Alvarez Nadir
Nummer 172899
Förderungsinstrument SNF-Förderungsprofessuren
Forschungseinrichtung
Département d'Ecologie et d'Evolution Faculté de Biologie et de Médecine Université de Lausanne
Muséum d'histoire naturelle
Hochschule Non Profit Organisationen (Bibliotheken, Museen, Akademien, Stiftungen) und Verwaltung - NPO
Hauptdisziplin Oekologie
Beginn/Ende 01.03.2017 - 31.03.2019
Bewilligter Betrag 592'434.00
Alle Daten anzeigen

Alle Disziplinen (4)

Disziplin
Oekologie
Botanik
Zoologie
Paläontologie

Keywords (12)

anthropogenic changes; spatially-explicit simulations; collection samples; macrofossils; Anthropocene; hyRNAD; genetic diversity; historical DNA; land-use change; next-generation-sequencing; climatic change; ancient DNA

Lay Summary (Französisch)

Lead
Malgré les efforts déployés pour identifier la nature et la gravité des menaces auxquelles font face de nombreuses espèces, nous avons encore une connaissance limitée de la dynamique de la biodiversité dans les perturbations anthropiques. Ici, nous cherchons à étudier les liens entre ces perturbations et la variation génétique au sein des espèces. Cette recherche se focalise sur une échelle de temps décennale (Anthropocène récent, i.e., époque post-industrielle).
Lay summary
Contenu et objectifs du travail de recherche
En utilisant des techniques de capture par hybridation à l'aide de sondes RAD, nous avons identifié une diminution de la diversité génétique au cours du dernier siècle dans une sauterelle suisse emblématique, montrant que les changements récents de l'utilisation des terres conduisent à des populations génétiquement érodées, diminuant le potentiel d'adaptation potentiel des espèces. En revanche, notre travail sur les macro-fossiles de sapin blanc indique que la diversité génétique et le potentiel d’adaptation est stable malgré l’impact de l’homme au début de l'Anthropocène (incendies, pâturage dans le sous-bois). Dans ce projet, nous analyserons la dynamique génétique des populations d’espèces sauvages au travers de trois perturbations environnementales documentées au cours de l’Holocène et l’Anthropocène. En plus de l'analyse de la variation neutre, nous analyserons la dynamique de la variation génétique potentiellement adaptative, en utilisant des sondes à base d'ARN messager (HyRAD-X). Pour le récent Anthropocène, nous analyserons deux papillons qui ont connu un fort déclin au cours du siècle dernier au Royaume-Uni. Pour l’Anthropocène ancien, nous étudierons des populations supplémentaires de sapin blanc pour confirmer nos précédents résultats. Enfin, nous comparerons l’effet des perturbations anthropogéniques aux perturbations climatiques naturelles pendant l’Holocène, en nous focalisant sur l’arolle et le mélèze au travers d’un épisode de froid survenu il y a environ 8000 ans.

Contexte scientifique et social du projet de recherche
Nos premiers succès avec l’application de HyRAD-X montrent le potentiel des données génomiques provenant de spécimens de collection et de macro-fossiles pour répondre à des questions écologiques et évolutives. Ici, nous visons à établir une nouvelle étape dans notre compréhension des conséquences des changements environnementaux passés et actuels sur la diversité génétique des espèces.

Direktlink auf Lay Summary Letzte Aktualisierung: 27.02.2017

Verantw. Gesuchsteller/in und weitere Gesuchstellende

Mitarbeitende

Publikationen

Publikation
Biotic drivers of river and floodplain geomorphology – new molecular methods for assessing present-day and past biota.
Larsen A Alvarez N Sperisen C Lane SN (2018), Biotic drivers of river and floodplain geomorphology – new molecular methods for assessing present-day and past biota., in Earth Surface Exchanges, 43(1), 333-338.
Long-term in situ persistence of biodiversity in tropical sky islands revealed by landscape genomics
Mastretta-Yanes A Xue AT Moreno-Letelier A Jorgensen TH Alvarez N Piñero D Emerson BC (2018), Long-term in situ persistence of biodiversity in tropical sky islands revealed by landscape genomics, in Molecular Ecology, 27(2), 432-448.
Preserving genetic connectivity in the European Alps protected area network.
Schoville SD Dalongeville A Viennois G Gugerli F Taberlet P Lequette B Alvarez N Manel S (2018), Preserving genetic connectivity in the European Alps protected area network., in Biological Conservation, 218, 99-109.
Spatial and temporal genetic dynamics of the endangered grasshopper Oedaleus decorus revealed by museum genomics.
Schmid S Pitteloud C Heckel G Pajkovic M Arlettaz R Alvarez N (2018), Spatial and temporal genetic dynamics of the endangered grasshopper Oedaleus decorus revealed by museum genomics., in Ecology & Evolution, 8(3), 1480-1495.
Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: The fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study.
Suchan T Espíndola A Emerson BC Gori K Dessimoz C Arrigo N Alvarez N (2017), Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: The fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study., in Molecular Phylogenetics and Evolution, 114, 189-198.
Elevation in tropical sky islands as the common driver in structuring genes and communities of freshwater organisms
Gueuning M Rutschmann S Suchan T Gattolliat J-L Jamsari A Kamil AI Pitteloud C Buerki S Balk (2017), Elevation in tropical sky islands as the common driver in structuring genes and communities of freshwater organisms, in Scientific Reports, 7, 16089.
Evidence for mega‐landslides as drivers of island colonization
García-Olivares V López H Alvarez N Machado A Emerson BC (2017), Evidence for mega‐landslides as drivers of island colonization, in Journal of Biogeography, 44(5), 1053-1064.
Genomics of extreme ecological specialists: multiple convergent evolution but no genetic divergence between ecotypes of Maculinea alcon butterflies
Koubínová D Dincă V Dapporto L Vodă R Suchan T Vila R Alvarez N (2017), Genomics of extreme ecological specialists: multiple convergent evolution but no genetic divergence between ecotypes of Maculinea alcon butterflies, in Scientific Reports, 7, 13752.
Global phylogeography of the insect pest Callosobruchus maculatus L. (Coleoptera: Bruchinae) relates to the history of its main host, Vigna unguiculata L.
Kébé K Alvarez N Tuda M Arnqvist G Fox CW Sembène M Espíndola A (2017), Global phylogeography of the insect pest Callosobruchus maculatus L. (Coleoptera: Bruchinae) relates to the history of its main host, Vigna unguiculata L., in Journal of Biogeography, 44, 2515-2526.
High rate of protein coding sequence evolution and species diversification in the lycaenids
Pellissier L Kostikova A Litsios G Salamin N Guisan A Alvarez N (2017), High rate of protein coding sequence evolution and species diversification in the lycaenids, in Frontiers in Ecology and Evolution, 5, 90.
Large-scale phylogenetic analysis of Amorphophallus (Araceae) derived from nuclear and plastid sequences reveals new subgeneric delineation
Claudel C Buerki S Chatrou LW Antonelli A Alvarez N Hetterscheid W (2017), Large-scale phylogenetic analysis of Amorphophallus (Araceae) derived from nuclear and plastid sequences reveals new subgeneric delineation, in Botanical Journal of the Linnean Society, 184(1), 32-45.
When different contact zones tell different stories: putative ring species in the Megachile concinna species complex (Hymenoptera: Megachilidae)
Ghazi Soltani G Bénon D Alvarez N Praz CJ (2017), When different contact zones tell different stories: putative ring species in the Megachile concinna species complex (Hymenoptera: Megachilidae), in Biological Journal of the Linnean Society, 121(4), 815-832.

Zusammenarbeit

Gruppe / Person Land
Formen der Zusammenarbeit
Finnish Museum of Natural History Finnland (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
Terrestrial Palaeoecology, Institute of Plant Sciences, University of Bern Schweiz (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
- Forschungsinfrastrukturen
AMIS Institute, Faculty of Médecine, University of Toulouse Frankreich (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
ancient DNA laboratory, WSL Birmensdorf Schweiz (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
- Forschungsinfrastrukturen
National History Museum, London Grossbritannien und Nordirland (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
Centre for GeoGenetics Dänemark (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation

Wissenschaftliche Veranstaltungen

Aktiver Beitrag

Titel Art des Beitrags Titel des Artikels oder Beitrages Datum Ort Beteiligte Personen
Colloquium of the AMIS institute Einzelvortrag hyRAD : a new molecular pipeline for performing genome complexity reduction on degraded DNA templates 27.04.2018 Toulouse, Frankreich Alvarez Nadir;
Colloquium of the Natural History Museum of Geneva Einzelvortrag New horizons for the study of historical DNA 12.01.2018 Geneva, Schweiz Alvarez Nadir;
Colloquium of the Institute of Systematic Botany, University of Zurich Einzelvortrag Combining capture and RAD-sequencing to unravel past genetic dynamics of tree species. 22.05.2017 University of Zurich, Schweiz Alvarez Nadir;
Colloquium of the Biodiversity and conservation Biology Research Unit, WSL Einzelvortrag Recent developments in the field of historical and ancient DNA analysis: prospects to decipher past population processes. 18.05.2017 Birmensdorf, Schweiz Alvarez Nadir;
5th Open Science PAGES Meeting (Past Global Changes): "Global Challenges for our Common Future: a paleoscience perspective" Vortrag im Rahmen einer Tagung Application of HyRAD-X, a method combining reduced representation of the exome and hybridization capture applied to ancient DNA to time series of subfossil needles unravels the early Anthropocene history of the silver fir, Abies alba, in a population from 07.05.2017 Zaragoza, Spanien Alvarez Nadir;
20th European Congress of Lepidopterology Poster A mirage of cryptic species: major mito-nuclear discordance uncovered by ddRAD-seq in Thymelicus sylvestris (Lepidoptera: Hesperiidae). 24.04.2017 Podgora, Kroatien Alvarez Nadir;


Selber organisiert

Titel Datum Ort
Joint MHNG-CJBG workshop on NGS techniques 07.05.2018 Geneva, Schweiz

Veranstaltungen zum Wissenstransfer

Aktiver Beitrag

Titel Art des Beitrags Titel des Artikels oder Beitrages Datum Ort Beteiligte Personen
Assemblée Générale de la Société des amis du Museum d'Histoire Naturelle de la Ville de Genève Vortrag 08.03.2018 Geneva, Schweiz


Auszeichnungen

Titel Jahr
‘unfunded A’ at the ERC-Consolidator call (LS8 panel) 2017

Verbundene Projekte

Nummer Titel Start Förderungsinstrument
126624 Coalescence and adaptation processes in plant-insect interactions: Bridging the gap between genomics and phylogeography 01.03.2010 Ambizione
144870 Consequences of species range contraction on the genetic diversity of cold-adapted organisms 01.03.2013 SNF-Förderungsprofessuren

Abstract

Significant research efforts and consequent media coverage have been devoted to the impacts of climate change on species distribution - but has this taken the spotlight off other human activities that are major threats to biodiversity? A recent analysis of over 8000 species on the IUCN red list shows that for about 80% of endangered species, climate change is not implicated in their extinction risk. While the Kyoto, Paris and Rio summits pave the way for a society with reduced greenhouse gas emissions, there are no equivalent agreements for other anthropogenic disturbances. Thus, there remains a need to understand and regulate non-climatic, human-induced changes on organisms and communities. Despite efforts to identify the nature and severity of threats facing many species, we still have limited knowledge of the dynamics of biodiversity throughout anthropogenic perturbations. Here, we aim at investigating links between such perturbations and genetic variation within species. This research would be done at both decadal (recent Anthropocene; i.e. post-industrial) and millennial time scales (early Anthropocene and Holocene; several thousand years ago). This two-scale study takes advantage of advances made during the first stage of my SNSF professorship; namely, two molecular pipelines that produce complexity-reduced genomic data from collection and macrofossil samples. These techniques allow leading-edge genomic technologies to be used with historical and ancient DNA (Hybridization Capture Using RAD Probes, i.e., hyRAD; and Hybridization Capture Using RNA-converted Exome-based RAD Probes, i.e., hyRNAD; respectively), irrespective of the level of sample preservation. Using hyRAD and hyRNAD, we have identified dramatic decreases in genetic diversity over the last 80 years in an iconic Swiss grasshopper, and two butterflies in Finland. These results show that recent land-use changes are leading to genetically depauperate populations, which may impact the putative adaptive potential of species. In contrast, our preliminary work on silver fir macrofossils from Origlio lake (Ticino, Switzerland) indicates that genetic diversity is stable through the early Anthropocene. Although large fires and cattle grazing have modified population sizes and dynamics in silver fir populations during this period, the adaptive potential of the species seems to have been maintained. In this second stage of my SNSF professorship, I aim to broaden our view of the consequences of land-use change during the early and recent Anthropocene. I will accomplish this through the inclusion of additional populations and species in broader comparative analyses. Specifically, I will investigate the fate of genetic variation of species over the course of environmental perturbations, using clasical as well as forward-time-model analyses of population genetics. In addition to the analysis of neutral variation as during the first stage of my SNSF professorship, here, I will analyze the dynamics of putatively adaptive genetic variation by applying exome-based RNA probes (i.e., HyRNAD) to the new set of studied populations and species. For the recent Anthropocene, we aim to analyze additional species of butterflies showing a strong decline over the last century in the UK (where there are detailed records of land-use). At the early Anthropocene scale, we will investigate additional populations of silver fir trees to identify whether the rule of stable genetic dynamics despite perturbations associated with fires and cattle grazing can be generalized. Finally, we will compare the effect of Anthropocene perturbations to natural Holocene climatic perturbations. We will accomplish this by comparing genetic dynamics during Anthropocene perturbations to a dramatic cold episode that occurred about 8000 years ago. This climatic event led to local extinctions in several mountain forest populations over at least 300 years. We will focus on two affected species: the European larch and the Arolla pine.Our proposed study will be a large-scale application of hyRNAD. Given our initial successes with these methods, we are confident that we can use time-series genomic data preserved in collection and macrofosil specimens to answer ecological and evolutionary questions. Our research will ultimately identify the impact of human-induced land-use changes on genetic diversity of organisms when facing different magnitudes of perturbations. More generally, we aim at setting a new milestone in our understanding of the consequences of past and current environmental changes on the in natura genetic diversity of species from temperate biomes.
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