Wildlife Genomics

The Wildlife Genomics group uses genetics and 'omics methods to determine the response of wild animals to environment variation

Integrating empirical and experimental approaches to studying drivers of adaptation and variation in biodiversity

Our research is typically founded on empirical data collection to quantify how environment variation can affect wildlife health. We use a combination of live-trapping, and where possible mark-release recapture or reciprocal transplant experiments, to obtain samples with which we can measure components of animal health and fitness, and/or potential for adaptation. To identify features of the environment that impact wildlife health, we acquire data about habitat and biodiversity, such as soil pollutants, diversity of free-living microbes, habitat structural diversity, available diet, and the types and prevalence of disease vectors and pathogens.

Empirical data collection in nature includes live trapping of rodents, collecting arthropod vectors, and biodiversity monitoring using environmental DNA (eDNA)
An Ugglan live trap placed near a rodent burrow is used to collect small rodents from which we obtain biomarkers of health; for example, hair and faecal samples allow us to quantify gut microbiota, diet, and the intestinal parasite community.	Flags are dragged along field transects and searched for ticks that are collected and screened for pathogens, such as the bacteria Borrelia burgdorferi that is the causative agent of Lyme disease.
Live trapping of rodents and biodiversity monitoring typically requires much sampling equipment (and a good field vehicle), which needs to be deployed in situ, checked and repacked - sometimes in challenging conditions.	Biodiversity at sample sites can be monitored in different ways (e.g. by habitat surveys, camera traps, acoustic monitoring), including the use of environmental DNA, which in this example was collected by passing water through a filter.

Experiments are used to examine how specific properties of the wildlife host and/or environmental features determine host fitness. For studies on small rodents, we release animals into field enclosures to readily monitor animals over time in a natural environment in which we can manipulate important components, such as exposure to pollution, feeding regime, and/or population density. Due to the excellent animal facilities at the University of Jyväskylä, we can readily create and maintain selection lines to determine the relative fitness of certain genotypes or phenotypes. 

Experimental field enclosures allow longitudinal monitoring of animals in a natural environment

Construction of field enclosures (image was taken soon after construction) located in the Chornobyl Exclusion Zone (CEZ), Ukraine allowed longitudinal monitoring of bank voles experiencing different levels of soil contamination (radionuclides) and thus a precise assessment of the effects of known doses of radiation exposure on wildlife health. This approach overcomes the biases associated with overlooking unsampled developmental stages (e.g. early life) of wild animals.

Field enclosures at Konnevesi Research Station are used for longitudinal monitoring of bank vole selection lines.

Our group is especially interested in understanding what properties of the host and/or its environment affect the host-associated microbiota (bacteria and fungi), with the goal of determining whether any change in microbiota would alter the provision of services to the host. An experimental microbiota facility is used to maintain cultures of gut microbiota (bacteria) in vitro. Experimental microbiota can be customised (e.g. by adding certain strains, or by dilution/use of antibiotics to remove strains) to alter the functional diversity of the community. Moreover, experimental microbiota can be transferred to animals (a faecal microbiota transplant) to afford an in vivo examination of the health effects of specific components of microbiota. Animals may be housed in Individual Ventilated Cages (IVCs) to prevent cross contamination of microbiota and subsequently released into experimental field enclosures to determine the relative performance of animals with different microbiota under natural conditions.

Use of an experimental microbiota facility allows creation of a customised microbiota to provide insights into diversity of functions provided by different taxa
	Individual Ventilated Cages (UVCs) are used to house small rodents without cross contamination of gut microbiota

Key measures of wildlife health or adaptation include differences in genome structure (e.g. in telomere length, mitochondrial DNA copy number and damage, genetic variation), transcriptional variation (e.g. by qPCR or RNAseq), changes in metabolites (e.g. in faecal or circulating short chain fatty acids or at untargeted metabolites), and/or pathogen burden (e.g. species of Borrelia, Anaplasma, Babesia); we also examine variation in the host-associated microbiota (bacteria and fungi) and associated aspects of gut health (e.g. cell type and mucus production, and transcription in the colon).

Quantifying anthropogenic impacts on the environment and wildlife health

Recent projects have have examined how anthropogenic impacts on the environment may scale to affect wildlife health. For example, we have studied the effects of terrestrial pollution such as radionuclides (derived from accidents at the nuclear power plants in Chornobyl, Ukraine, and Fukushima, Japan) or metals (as by-products of mining/smelting activities). 

We also study how urban development impacts wildlife health through its affects on forest biodiversity, and we are actively studying whether biodiversity restoration (e.g. via rewilding) would impact biodiversity and disease burden in wildlife.

Projects sample sites are typically forest habitats located in Finland, and also Ukraine, and in the UK

Forest and grassland, and a warning sign, located within the Chornobyl Exclusion Zone (CEZ), Ukraine

Field site located in the Forth Valley, Scotland, UK that is monitored as part of the project BEPREP

Use of diverse genetics and 'omics technologies

We principally use and analyse data from next generation sequencing (NGS) technologies, for example use of RNAseq, amplicon sequencing (at 16S, ITS, and 18S loci), and metagenomics, to quantify transcriptional changes, variation in microbiota (e.g. bacteria, fungi) or diet/parasites, and to uncover functional variation in bacterial metagenomes; we also use ddRAD or shallow genome sequencing to characterise genome-wide genetic variation. While we mostly use Illumina NGS, we nonetheless utilise other short read (Ion Torrent) and long read (Pacific Biosciences, Oxford Nanopore) technologies when they are more appropriate to the project's goals.

We use stable isotope analyses to determine wildlife diet, and targeted and apply untargeted metabolomics to quantify, for example, inter-individual differences in host physiology and microbiota function.

We apply quantitative PCR (qPCR) to determine variation in gene expression, copy number (e.g. telomere length, ribosomal rRNA locus copy number, and mitochondrial DNA content/damage), and pathogen burden.