Determining the subspecies composition of bean goose harvests in Finland using genetic methods

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 (ɸ ST = 0.11-0.20) but none with the nuclear microsatellite markers (all pairwise F ST-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 H E = 0.69) and there were no signs of past population size reductions, although significantly positive inbreeding coefficients in all sampling sites (F IS = 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 (Anser brachyrhynchus). The current population is not under threat by genetic impoverishment but monitoring in the future is desirable.

Seasonal and diel activity patterns of the endangered taiga bean goose (Anser fabalis fabalis) during the breeding season, monitored with camera traps

Taiga bean goose (Anser fabalis fabalis) is an endangered subspecies that breeds sporadically in remote habitats in the arctic and boreal zones. Due to its elusive behaviour, there is a paucity of knowledge on the behaviour of taiga bean goose during the breeding season, and survey methods for monitoring numbers in the breeding areas are lacking. Camera traps are a useful tool for wildlife monitoring, particularly when there is a need for non-invasive methods due to the shy nature of the species. In this study, we tested the use of camera traps to investigate seasonal and diel activity patterns of taiga bean goose in Finland over two successive breeding seasons, 2018 and 2019. We did this by modelling counts of geese from images with generalized linear and additive mixed models. The camera type (cameras placed by experts specialized in bean goose ecology vs randomly placed cameras) did not influence the count of taiga bean goose (p = 0.386). However, the activity varied significantly by region, Julian day, time of day and temperature, with the study site (individual peatland) and year adding substantial random variation and uncertainty in the counts. Altogether, the best fitting model explained nearly 70% of the variation in taiga bean goose activity. The peak in activity occurred about a month later in the southernmost region compared to the more northern regions, which may indicate behaviours related to migration rather than breeding and moulting. Our results show that long-term monitoring with game camera traps provide a potential unobtrusive approach for studying the behavioural patterns of taiga bean goose and can increase our ecological knowledge of this little-known subspecies. The results can be applied to planning of the annual censuses and finding the optimal time frame for their execution.

Lack of conspicuous sex-biased dispersal patterns at different spatial scales in an Asian endemic goose species breeding in unpredictable steppe wetlands

Dispersal affects the spatial distribution and population structure of species. Dispersal is often male-biased in mammals while female-biased in birds, with the notable exception of the Anatidae. In this study, we tested genetic evidence for sex-biased dispersal (SBD) in the Swan Goose Anser cygnoides, an Asian endemic and IUCN vulnerable species, which has been increasingly restricted to breeding on Mongolian steppe wetlands. We analyzed the genotypes of 278 Swan Geese samples from 14 locations at 14 microsatellite loci. Results from assignment indices, analysis of molecular variance, and five other population descriptors all failed to support significant SBD signals for the Swan Goose at the landscape level. Although overall results showed significantly high relatedness within colonies (suggesting high levels of philopatry in both sexes), local male genetic structure at the 1,050 km distance indicated greater dispersal distance for females from the eastern sector of the breeding range. Hence, local dispersal is likely scale-dependent and female-biased within the eastern breeding range. These findings are intriguing considering the prevailing expectation for there to be female fidelity in most goose species. We suggest that while behavior-related traits may have facilitated the local genetic structure for the Swan Goose, several extrinsic factors, including the decreasing availability of the nesting sites and the severe fragmentation of breeding habitats, could have contributed to the absence of SBD at the landscape level. The long-distance molt migration that is typical of goose species such as the Swan Goose may also have hampered our ability to detect SBD. Hence, we urge further genetic sampling from other areas in summer to extend our results, complemented by field observations to confirm our DNA analysis conclusions about sex-specific dispersal patterns at different spatial scales in this species.

Recent introgression between Taiga Bean Goose and Tundra Bean Goose results in a largely homogeneous landscape of genetic differentiation

Several studies have uncovered a highly heterogeneous landscape of genetic differentiation across the genomes of closely related species. Specifically, genetic differentiation is often concentrated in particular genomic regions (“islands of differentiation”) that might contain barrier loci contributing to reproductive isolation, whereas the rest of the genome is homogenized by introgression. Alternatively, linked selection can produce differentiation islands in allopatry without introgression. We explored the influence of introgression on the landscape of genetic differentiation in two hybridizing goose taxa: the Taiga Bean Goose (Anser fabalis) and the Tundra Bean Goose (A. serrirostris). We re-sequenced the whole genomes of 18 individuals (9 of each taxon) and, using a combination of population genomic summary statistics and demographic modeling, we reconstructed the evolutionary history of these birds. Next, we quantified the impact of introgression on the build-up and maintenance of genetic differentiation. We found evidence for a scenario of allopatric divergence (about 2.5 million years ago) followed by recent secondary contact (about 60,000 years ago). Subsequent introgression events led to high levels of gene flow, mainly from the Tundra Bean Goose into the Taiga Bean Goose. This scenario resulted in a largely undifferentiated genomic landscape (genome-wide F_ST = 0.033) with a few notable differentiation peaks that were scattered across chromosomes. The summary statistics indicated that some peaks might contain barrier loci while others arose in allopatry through linked selection. Finally, based on the low genetic differentiation, considerable morphological variation and incomplete reproductive isolation, we argue that the Taiga and the Tundra Bean Goose should be treated as subspecies.

Over a Thousand Years of Evolutionary History of Domestic Geese from Russian Archaeological Sites, Analysed Using Ancient DNA

The European domestic goose is a widely farmed species known to have descended from the wild greylag goose (Anser anser). However, the evolutionary history of this domesticate is still poorly known. Ancient DNA studies have been useful for many species, but there has been little such work on geese. We have studied temporal genetic variation among domestic goose specimens excavated from Russian archaeological sites (4th–18th centuries) using a 204 base pair fragment of the mitochondrial control region. Specimens fell into three different genetic clades: the domestic D-haplogroup, the F-haplogroup that includes both wild and domestic geese, and a clade comprising another species, the taiga bean goose. Most of the subfossil geese carried typical domestic D-haplotypes. The domestication status of the geese carrying F-haplotypes is less certain, as the haplotypes identified were not present among modern domestic geese and could represent wild geese (misclassified as domestics), introgression from wild geese, or local domestication events. The bones of taiga bean goose were most probably misidentified as domestic goose but the domestication of bean goose or hybridization with domestic goose is also possible. Samples from the 4th to 10th century were clearly differentiated from the later time periods due to a haplotype that was found only in this early period, but otherwise no temporal or geographical variation in haplotype frequencies was apparent.