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