Genetic assessment reveals inbreeding, possible hybridization, and low levels of genetic structure in a declining goose population

The population numbers of taiga bean goose (Anser fabalis fabalis) have halved during recent decades. Since this subspecies is hunted throughout most of its range, the decline is of management concern. Knowledge of the genetic population structure and diversity is important for guiding management and conservation efforts. Genetically unique subpopulations might be hunted to extinction if not managed separately, and any inbreeding depression or lack of genetic diversity may affect the ability to adapt to changing environments and increase extinction risk. We used microsatellite and mitochondrial DNA markers to study the genetic population structure and diversity among taiga bean geese breeding within the Central flyway management unit using non-invasively collected feathers. We found some genetic structuring with the maternally inherited mitochondrial DNA between four geographic regions (ɸST = 0.11-0.20) but none with the nuclear microsatellite markers (all pairwise FST-values 0.002- 0.005). These results could be explained by female natal philopatry and male-biased dispersal, which completely homogenizes the nuclear genome. Therefore, the population could be managed as a single unit. Genetic diversity was still at a moderate level (average HE = 0.69) and there were no signs of past population size reductions, although significantly positive inbreeding coefficients in all sampling sites (FIS = 0.05-0.10) and high relatedness values (r = 0.60-0.86) between some individuals could indicate inbreeding. In addition, there was evidence of either incomplete lineage sorting or introgression from the pink-footed goose (A. brachyrhynchus). The current population is not under threat by genetic impoverishment but monitoring in the future is desirable.

Methods
We collected bean goose (Anser fabalis) feathers from nests or brood-rearing/moulting sites in Finland or close to the Finnish border (Sør-Varanger municipality, Norway) using mostly citizen-science approach during the years 2006-2014 and 2016-2018. In addition, we included feathers collected from taiga bean geese (A. f. fabalis) handled for ringing in Finland in the years 2017-2018. We also sampled other goose populations for comparative purposes: 1. Swedish breeding taiga bean geese (2014; n = 7), 2. migrating Russian taiga bean geese hunted from Finland or Estonia (2010-2012, 2017; n = 7), 3. Norwegian breeding tundra bean geese (A. f. rossicus; 2002, 2006; n = 7) and 4. Iceland breeding pink-footed geese (A. brachyrhynchus; the Natural History Museum of Reykjavik; n = 7).

DNA from a calamus and from a blood clot (when visible) was extracted using QuickExtract DNA Extraction Solution (Lucigen) according to the manufacturer’s protocol, except for a 15 min incubation at 65 ⁰C instead of 6 min. We genotyped the samples for 28 microsatellite loci in four multiplex reactions. The microsatellite loci were amplified using Multiplex PCR Kit (Qiagen) in 6 µl reaction volumes according to manufacturer’s protocol with 1 µl of template DNA. We performed fragment analysis with an ABI 3730 and scored the alleles using GeneMapper 5 (Applied Biosystems). We excluded six loci due to missing data, lack of polymorphism, high frequency of null-alleles or deviation from Hardy-Weinberg equilibrium, thus leaving with a final dataset of 22 loci. Based on molecular sexing, relatedness and parentage analyses, a subset of the dataset was formed, from which inferred closely related kin (parent(s) of offspring, all but one sibling and individuals showing signs of inbreeding) were removed.