DOI: 10.5061/dryad.7wm37pvv6
title: Genetic assessment reveals inbreeding, possible hybridization, and low levels of genetic structure in a declining goose population

description: 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.
description: We collected bean goose (<em>Anser
 fabalis</em>) 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 (<em>A. f. fabalis</em>) 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;
 <i>n</i> = 7), 2. migrating Russian taiga bean geese hunted
 from Finland or Estonia (2010-2012, 2017; <i>n</i> = 7), 3.
 Norwegian breeding tundra bean geese (<em>A. f.
 rossicus</em>; 2002, 2006; <i>n</i> = 7) and 4. Iceland
 breeding pink-footed geese (<em>A. brachyrhynchus</em>; the
 Natural History Museum of Reykjavik; <i>n</i> = 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.
description: File 1. Full dataset. Microsatellite genotype results in
 Genepop-format for 488 taiga bean goose (<em>Anser fabalis
 fabalis</em>) sampled from Finland or close to Finnish border
 from Norway for 22 loci. The aforementioned microsatellite loci were used
 to identify the inviduals from field collected feather samples. Data is
 divided into four populations based on geographical locations (Western
 Finland, Eastern Finland/Kainuu, Northern-Ostrobothnia/Southern Lapland
 and Lapland; in this order in the Genepop-file), see Figure 3 in
 the published article for the regions. 000 denotes missing
 value. File 2. Non-kin dataset. A subset of the full
 dataset, from which closely related individuals (parent(s), all but one
 sibling and potentially inbred individuals) were removed resulting in 376
 individuals. Formatted as the full dataset. File
 3. Tundra bean goose (<em>A. f. rossicus</em>) and dead goose
 with pink-footed goose (<em>A. brachyrhynchus</em>) mtDNA
 sampled from Finland. Microsatellite genotype results in
 Genepop-format for samples which were exluded from other analyses (except
 for hybridization analyses) based on mitochondrial DNA. Genotypes are
 shown for 22 loci for tundra bean geese and a single goose which was found
 dead and harbored pink-footed goose mitochondrial DNA. See Figure 3 of
 the published article for sampling locations. 000 denotes missing
 value. File 4. Outgroups. Microsatellite genotype
 results in Genepop-format for seven migrating Russian taiga bean geese
 hunted from Finland or Estonia, seven Swedish breeding taiga bean geese,
 seven Norwegian breeding tundra bean geese and seven Iceland breeding
 pink-footed geese (in this order in the Genepop-file). See Figure 3 of
 the published article for sampling locations. 000 denotes missing
 value. File 5. README-file