Research On Natural Epigenetic Diversity And Its Influencing Factors In Three Bat Species

Biodiversity faces challenges from habitat fragmentation, over exploitation, and globalclimate change. Organisms have to adjust their phenotype in responding to variousenvironmental stresses. Recent studies showed that epigenetic modifications have animportant role in mediating environmentally induced phenotypic variation, and thoseepigenetic variances could be inherited by future generations. Therefore, epigenetic processesare considered as another source of the natural heritable variation, and another dimension inevolution. Crucial steps before estimating the potential role of epigenetic variation inproducing new phenotypes and responding to global environmental change for organisms,are exploring the genomic epigenetic diversity in natural populations and finding itsinfluencing factors.DNA methylation is one of the best studied epigenetic mechanisms, and has a criticalrole in many key biological processes. Till now, related researches have been done in wildplant populations; however, limited data are explored in wild animals, and only3studiesabout population epigenetic diversity were reported on steelhead (Oncorhynchus mykiss),redbelly dac (Chrosomus eos-neogaeus), and house sparrows (Passer domesticus). Thereis no study about population epigenetic has been done on wild mammal populationsyet, while mammals have special evolution mechanisms to adapt to varied environments,and they may have different epigenetic processes in responding to environmental variationscomparing with other animals. Thus, it’s necessary to explore the population epigeneticdiversity of wild mammals. Bats have large populations, wide distributions, significantecological functions, and are sensitive to environmental variance; therefore, they may presentan opportunity to explore epigenetic variance in natural mammalian populations.Considering that there exist difference of DNA methyaltion among different tissues,developments, and behaviors, we extracted genomic DNA from muscle tissues of131female,adult and non-hibernate individuals in3bat species: Rhinolophus pusillus, Hipposiderosarmiger, and Miniopterus fuliginosus. Using methylation-sensitive amplified polymorphism(MSAP) technique, we obtained more than800bands in each species to explore thesequestions in bat populations: what’s the level and polymorphism of genome-wide DNAmethylation, whether DNA methylation diversity is significant structured into distinctbetween-and within-population components and whether it is significant correlated withgenetic diversity, geographic distance, and environmental factors, e.g. coordinates, climatefactors, human disturbance, roosting size, concealed degree and plant types. The maincontexts were as follows:1. The methylation levels in3bats were,20.1-24.2%in R. pusillus,20.4-26.5%in H.armiger, and20.6-22.0%in M. fuliginosus. There existed extensive methylation variationbut low level in genetic variation in those bat populations, and epigenetic diversity exceeded conventional genetic diversity when the two magnitudes are compared using the Shannonindex, implying that at least partly epigenetic variance is dependent from genetic variance.Similar results were found in wild plant populations, implied that extensive intraspecificepigenetic variation found in our study is probably widespread in wild populations, andsupports an alternative system for organism in responding to natural variation.2. There were about5.0%,30.7%and24.6%methylated loci were significantdifferentiation among populations in R. pusillus, H. armiger, and M. fuliginosus, respectively,indicating estensive epigenetic differentiation among populations in each species.Between-group eigen analyses (BGEA) showed significant epigenetic structure existing ineach bats based on multilocus epigenetic population differentiation, i.e. methylation-basedepigenetic variation was structured into distinct between-and within-population components,implying extensive individual epigenotypic variation, which is a critical prerequisite forepigenetic variation to have some microevolutionary potential.3. Both co-inertia analysis and Mantel tests (controlling geographic distance andenvironmental variables) showed that epigenetic variance was significant correlated withgenetic profile in those3bats, implying epigenetic variance is dependent to genetic variation.However, low genetic flow and epigenetic flow among populations implied that neutral driftcould also result in epigenetic variations.4. Sequential forward selection analysis showed that latitude (pseudo-F=2.162, P=0.044) had signifiant effects on epigenetic diversity among R. pusillus populations andaccounted for22.2%variance; mean annual humidity (pseudo-F=2.130, P=0.028) andconcealed degree of caves (pseudo-F=2.025，P=0.059) had marginally significant effectson epigenetic difference between H. armiger populations and accounted for42.8%variance;plant types(pseudo-F=3.128，P=0.014), roosting size (pseudo-F=2.000，P=0.023), andhuman disturbance (pseudo-F=1.932，P=0.094) had significant or marginally significanteffects on population epigenetic difference, accounting altogether for68.3%variance. Aboveresults indicated that environmental factors had significant effects on epigenetic diversity infemale bats populations. Therefore, epigenetic mechanism is an alternative system for bats toresponse to environmental variance, or bats could adapt to new environment via DNAmethylation variance.The bat populations have high level epigenetic diversities, which were affected bycorresponding genetic diversity, neutral drift, and environmental changes. It’s beneficial forbat species in improving their tolerance by epigenetic mechanisms in evolution, however, thepopulation size of bats are reduced by negative effects from global climate change, andhabitat destruction, which are induced by human activities. Thus, we still need to reducenegative disturbances to bats.