Three Molecular Markers Show No Evidence of Population Genetic Structure in the Gouldian Finch (Erythrura gouldiae)

As the Goose Flies: Migration Routes and Timing Influence Patterns of Genetic Diversity in a Circumpolar Migratory Herbivore

Migration schedules and the timing of other annual events (e.g., pair formation and molt) can affect the distribution of genetic diversity as much as where these events occur. The greater white-fronted goose (Anser albifrons) is a circumpolar goose species, exhibiting temporal and spatial variation of events among populations during the annual cycle. Previous range-wide genetic assessments of the nuclear genome based on eight microsatellite loci suggest a single, largely panmictic population despite up to five subspecies currently recognized based on phenotypic differences. We used double digest restriction-site associated DNA (ddRAD-seq) and mitochondrial DNA (mtDNA) sequence data to re-evaluate estimates of spatial genomic structure and to characterize how past and present processes have shaped the patterns of genetic diversity and connectivity across the Arctic and subarctic. We uncovered previously undetected inter-population differentiation with genetic clusters corresponding to sampling locales associated with current management groups. We further observed subtle genetic clustering within each management unit that can be at least partially explained by the timing and directionality of migration events along with other behaviors during the annual cycle. The Tule Goose (A. a. elgasi) and Greenland subspecies (A. a. flavirostris) showed the highest level of divergence among all sampling locales investigated. The recovery of previously undetected broad and fine-scale spatial structure suggests that the strong cultural transmission of migratory behavior restricts gene flow across portions of the species’ range. Our data further highlight the importance of re-evaluating previous assessments conducted based on a small number of highly variable genetic markers in phenotypically diverse species.

Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing

BACKGROUND

Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS.

RESULTS

In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA.

CONCLUSIONS

Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.