EVOLHAB: A genomic approach to evaluate the effects of habitat instability on the evolutionary dynamics of insular lineages
In the era of rapid environmental change, understanding the role of habitat persistence in the evolutionary dynamics and endemicity of insular lineages, can be crucial for preserving island biodiversity. EVOLHAB aims to disentangle the effects of habitat instability on demographic history, species diversification and molecular evolution.
In the era of rapid environmental change, understanding the role of habitat persistence in the evolutionary dynamics and endemicity of insular lineages, can be crucial for preserving island biodiversity. EVOLHAB aims to disentangle the effects of habitat instability on demographic history, species diversification and molecular evolution.
The QUESTION
The potential effects of habitat persistence on evolutionary dynamics is a long-standing question at the interface between ecology and evolutionary biology that has not been sufficiently addressed due to scarcity of suitable study systems and analytical limitations. Previous studies proposed that habitat instability selects for higher dispersal propensity resulting in larger species ranges, while long-term habitat stability promotes lower dispersal and smaller species ranges. An alternative view focuses on higher rates of local population extinction and strong population bottlenecks in ephemeral habitats vs. long-term population persistence in stable habitats. In either case, such habitat-induced differences in demographic processes are expected to affect both lineage diversification and molecular evolution, but the empirical evidence remains limited and controversial.
our approach
EVOLHAB aims to provide insights into the effects of habitat persistence on evolutionary dynamics by focusing on highly suitable non-model organisms and applying a combination of high-throughput DNA sequencing approaches that will allow us to address these questions at multiple levels: genome-wide SNP data (from ddRADseq) for fine-scale population analyses, low-coverage Whole Genome Sequencing for phylogenomics and DNA metabarcoding for comparative analyses at the community level.
objectives
Objective 1: Assess the effect of habitat persistence on population dynamics across distinct insular settings.
EVOLHAB uses genome-wide SNP data to perform side-by-side comparisons of population structure, genetic diversity and demographic history between co-distributed pairs of psammophilous vs. geophilous lineages of the genus Eutagenia (Coleoptera: Tenebrionidae). Psammophilous (sand-obligate) lineages are associated with unstable sandy coastal habitats, while geophilous (hard-soil substrate) lineages are associated with comparatively stable inner habitats (shrublands, maquis and Mediterranean forests).
EVOLHAB uses genome-wide SNP data to perform side-by-side comparisons of population structure, genetic diversity and demographic history between co-distributed pairs of psammophilous vs. geophilous lineages of the genus Eutagenia (Coleoptera: Tenebrionidae). Psammophilous (sand-obligate) lineages are associated with unstable sandy coastal habitats, while geophilous (hard-soil substrate) lineages are associated with comparatively stable inner habitats (shrublands, maquis and Mediterranean forests).
Objective 2: Evaluate the effect of habitat association on molecular evolution and lineage diversification.
For this purpose, EVOLHAB uses a set of at least 1,000 genome-wide coding loci to reconstruct a time-calibrated phylogeny including all the main insular lineages of the genus Eutagenia from the Eastern Mediterranean and additional lineages from mainland Greece and Turkey. Substitution rate metrics (total, synonymous [dS], non-synonymous [dN], and the dN/dS ratio [ω]) for each locus and their average rate across the genome will be computed for both psammophilous and geophilous lineages of Eutagenia and we will test for correlation of those metrics with lineage net diversification and effective population size estimates.
For this purpose, EVOLHAB uses a set of at least 1,000 genome-wide coding loci to reconstruct a time-calibrated phylogeny including all the main insular lineages of the genus Eutagenia from the Eastern Mediterranean and additional lineages from mainland Greece and Turkey. Substitution rate metrics (total, synonymous [dS], non-synonymous [dN], and the dN/dS ratio [ω]) for each locus and their average rate across the genome will be computed for both psammophilous and geophilous lineages of Eutagenia and we will test for correlation of those metrics with lineage net diversification and effective population size estimates.
Objective 3: Evaluate the effects of habitat instability at the assemblage level.
While the previous two objectives focus on the genus Eutagenia as a model system, the third objective broadens the spectrum to entire sand-dwelling beetle assemblages of the sandy coastal habitats of Cyprus, including > 30 sand-obligate taxa and habitat generalists found consistently in the sandy shore habitats. For this purpose, we will sample systematically 10 sand dune ecosystems of different sizes and grades of disturbance along the coast of Cyprus using pitfall traps. We will then apply whole-organism community mtDNA metabarcoding to obtain haplotype-level data (i.e., Amplicon Sequence Variants; ASVs) for each of the sampled beetle taxa. Based on the ASV data, we will estimate intrapopulation genetic diversity and metrics of population differentiation for each species, we will reconstruct haplotype networks and we will apply model-based approaches to test for concerted demographic responses.
While the previous two objectives focus on the genus Eutagenia as a model system, the third objective broadens the spectrum to entire sand-dwelling beetle assemblages of the sandy coastal habitats of Cyprus, including > 30 sand-obligate taxa and habitat generalists found consistently in the sandy shore habitats. For this purpose, we will sample systematically 10 sand dune ecosystems of different sizes and grades of disturbance along the coast of Cyprus using pitfall traps. We will then apply whole-organism community mtDNA metabarcoding to obtain haplotype-level data (i.e., Amplicon Sequence Variants; ASVs) for each of the sampled beetle taxa. Based on the ASV data, we will estimate intrapopulation genetic diversity and metrics of population differentiation for each species, we will reconstruct haplotype networks and we will apply model-based approaches to test for concerted demographic responses.
COASTAL SAND DUNES
Sandy shores are highly dynamic environments, due to their unstable substrate and their constant change in response to wind, waves, tides and sea-level fluctuations. Their faunas and floras, including many sand-obligate species, are thus exposed to temporally variable and often harsh conditions. Sandy beaches and coastal sand dunes are of high relevance in the era of rapid environmental change, as they offer key ecosystem services (e.g., storm buffering, nutrient cycling), while they are highly threatened by anthropogenetic activities and sea-level rise. Climate change is predicted to affect greatly the distribution and survival of sandy shore populations, increasing the risk of local extirpations and global extinctions of psammophilous species, especially if they indeed have low levels of genetic diversity due to repeated population bottlenecks. In Cyprus, although the great majority of the coastal sandy ecosystems are highly disturbed due to strong anthropogenic pressures, they remain very poorly studied. A high percentage of Cyprus’ sand dune flora is considered threatened, but information on the sand-dwelling invertebrate fauna is largely lacking. EVOLHAB aims to provide insights into the effects of both natural and anthropogenic disturbance on the terrestrial fauna of sandy shores and the potentially reduced genetic diversity of sand-obligate species, which is expected to stimulate further research on the biota of those vulnerable ecosystems, as well as to promote public awareness and future conservation initiatives.
The project EXCELLENCE/0421/0419 is co-financed by the European Regional Development Fund and the Republic of Cyprus through the Research and Innovation Foundation.