Vicki L. Friesen

Population assignment methods enable biodiversity managers to identify the population origins of individuals or samples, which can help to determine the population‐specific impacts of human activities. Although population assignment is a powerful tool, accuracy can be low when populations have unequal odds of being sampled, which may arise from factors such as differences in population sizes, migration patterns, or behavior. When the probability of being assigned to population 1 given the individual is from population 1, , is assumed to be equal to the probability of being from population 1 given that the individual is assigned to population 1 , assignment confidence will be overinflated if the probability of sampling differs between groups. One potential consequence of this overconfidence could be inaccurate delineation of protected areas. To assess the reliability of population assignment, the relevant probability must be used: the probability that an individual belongs to a population given that it was assigned to the population. Understanding and calculating this conditional probability is essential to avoid misinterpretation of results. We demonstrate how to calculate conditional probabilities for assignments, and to identify the conditions under which the ability to assign individuals accurately is poor. We also demonstrate how the probability of correct assignment can be low when dealing with unequally sampled populations. To mitigate these issues, we suggest using population assignment with multiple sources of data and in conjunction with other methods to improve population assignment.

Speciation in marine taxa is dynamic and complex, often occurring in the absence of absolute geographic barriers to gene flow. Boobies comprise a clade of seven highly mobile seabird species with high diversity in the eastern Pacific Ocean, where no land barriers separate extant sister species and hybridization is widespread. They exhibit striking diversity in bare-part coloration, an important signal of mate quality, and possess a novel multiple sex chromosome system (Z ₁ Z ₂ Z ₁ Z ₂ / Z ₁ Z ₂ W), likely resulting from a fusion between an ancestral autosomal microchromosome and the W chromosome. To understand speciation processes in the context of gene flow, we sequenced and analyzed 29 short-read booby genomes and assembled a reference northern gannet genome to (1) test for introgression, (2) characterize genomic patterns of divergence across species, and (3) investigate the gene content and evolution of the neo-sex chromosome. We found that divergence among eastern Pacific sister taxa is temporally associated with periods of glacial maxima. Between periods of glacial maxima, two pairs of sister species (blue-footed and Peruvian boobies; masked and Nazca boobies) exhibit strong signatures of episodic introgression, indicating that speciation has occurred over multiple periods of divergence followed by gene flow. However, in the third pair of sister species, genomic signatures showed higher divergence within brown booby populations than between brown and Cocos boobies. We also identified the epidermal differentiation complex – a gene cassette involved in skin, feather, beak, and claw development – on the neo-sex region of the W chromosome, where it spans the boundary between the putatively recombining and non-recombining regions, with interspecific variation in the exact recombination suppression boundary. We inferred that this complex may contribute to diversity in feather and bare part coloration across boobies. Together, these results reveal that diversification and speciation in a clade of highly mobile seabirds emerged from a complex evolutionary history involving historical climate dynamics, introgression, and sex chromosome evolution.

Identifying genetically differentiated populations is important for successful species conservation and management, and collecting baseline population genomic data can allow us to quantify impacts from environmental changes and anthropogenic stressors. Unlike most auks, which breed in a few large colonies, black guillemots ( Cepphus grylle ) are dispersed breeders, whose range spans diverse environmental conditions, from polar to temperate waters. They are harvested in some northern regions and can be an important indicator of coastal ecosystem health, but knowledge of their population genetic structure is limited. We used double‐digest restriction‐site associated DNA sequencing to determine the extent to which regional samples of black guillemots ( n = 172) in the Arctic and North Atlantic oceans differ at presumptively neutral markers. Population genetic analyses identified three genetic clusters: (1) Northwest Atlantic: Gulf of Maine, Gulf of St. Lawrence, and East Canadian Shelf (Nova Scotia); (2) Arctic: Baffin Bay, Hudson Bay, Davis Strait, Labrador Shelf, East Canadian Shelf (Newfoundland), and Fram Strait (Svalbard); and (3) Northeast Atlantic: Denmark Strait (Iceland) and the Baltic Sea. Regions of secondary contact appear to exist in northern Baffin Bay and the Northwest Atlantic. Possible reasons for this pattern of genetic structure include historical isolation in multiple glacial refugia during the Pleistocene and contemporary barriers to gene flow. Comparison of several potential historical scenarios provided strongest support for isolation of black guillemots in two glacial refugia in the Northwest and Northeast Atlantic, followed by range expansion and secondary contact in the Arctic since recession of the glaciers. Our results suggest that management of black guillemots will require an internationally coordinated approach to conserve the genomic variation within this species.

Halogenated flame retardants (HFRs) are chemical additives used in many household and commercial products. Due to their persistence, long-range transport, bioaccumulative potential, and toxicity, several HFRs were listed for elimination or restrictions under the international Stockholm Convention on Persistent Organic Pollutants (SC-POPs). To understand how levels of HFRs in the environment have changed since being listed under the SC-POPs, herring gull ( Larus argentatus ) eggs were collected from 17 colonies across Canada (Laurentian Great Lakes, Niagara and St. Lawrence rivers, and Atlantic and Arctic regions) from 2008–2023. Eggs were analyzed for SC-POPs-listed HFRs; total-α-hexabromocyclododecane (HBCDD), Σpolybrominated diphenyl ethers (PBDEs; sum concentration of 11 tri- to hepta-BDE congeners), BDE-209, and ΣDechlorane Plus (DP; sum concentration of syn- and anti- isomers). Overall, no significant temporal changes in concentrations of the four target classes of HFRs were found for most comparisons across colonies (75%, 51/68). Significant declines were found for 13% of class-colony comparisons while BDE-209 concentrations increased significantly at one colony. Evidence of a significant influence of the SC-POPs on concentrations was equivocal, with 6% of trends declining with the year of nomination, year of listing, or before the year of nomination, and 4% of trends showing increases. Despite more than a decade of regulation for some of these compounds, herring gulls continue to be exposed to HFRs, presumably from sources such as stockpiles, discarded products, or re-release from environmental reservoirs. Continued multi-site monitoring of HFRs is required to fully assess the effectiveness of regulations that may take several decades to show consistent evidence of reduced exposure in gulls.

The ability to assign biological samples to source populations with high accuracy and precision based on genetic variation is important for numerous applications from ecological studies through wildlife conservation to epidemiology. However, population assignment when genetic differentiation is low is challenging, and methods to address this problem are lacking. The application of artificial neural networks to population assignment using genomic data is highly promising. Here we present popfinder: a new, easy‐to‐use Python‐based artificial neural network pipeline for genetic population assignment. We tested popfinder both with simulated genetic data from populations connected by varying levels of gene flow and with reduced‐representation sequence data for three species of seabirds with weak to no population genetic structure. Popfinder was able to assign individuals to their source populations with high accuracy, precision and recall in most cases, including both simulated and empirical data sets, except in the empirical data set with the weakest population structure, where the comparator programs also performed poorly. Compared to other available software, popfinder was slower on the simulated data sets due to hyperparameter tuning and the fact that it does not reduce the dimensionality of the data set; however, all programs ran in seconds on empirical data sets. Additionally, popfinder provides a perturbation ranking method to help develop optimised SNP panels for genetic population assignment and is designed to be user‐friendly. Finally, we caution users of all assignment programs to watch both for leakage of data during model training, which can lead to overfitting and inflation of performance metrics, and for unequal detection probabilities.

For long‐lived species with biparental care, coordination and compatibility in the foraging behavior of breeding mates may be crucial to successfully raise offspring. While high foraging success is clearly important to reproductive success, it might be equally important that the mate has a complementary foraging strategy. We test whether breeding partners have similar or dissimilar foraging strategies in a species where both partners share breeding responsibilities and exhibit high mate fidelity (thick‐billed murre; Uria lomvia). To examine whether thick‐billed murres showed complementary in foraging strategies, we attached GPS accelerometers to both partners within 40 thick‐billed murre chick‐rearing pairs. Individuals within a breeding pair were dissimilar in their foraging trip distance and in their number of dives during foraging trips compared to randomized pairs. Breeding partners were also more similar in wing length than randomized pairs. This result could be related to individual quality as individuals select similar sized partners or select sites that lead to similar sized partners. We conclude that foraging strategy diversity could be maintained in this population either because individuals prefer partners with foraging strategies complementary to their own, or because partners diverge in foraging strategies over multiple breeding season together.

Genetic diversity can influence fitness components such as survival and reproductive success. Yet the association between genetic diversity and fitness based on neutral loci is sometime very weak and inconsistent, with relationships varying among taxa due to confounding effects of population demography and life history. Fitness-diversity relationships are likely to be stronger and more consistent for genes known to influence phenotypic traits, such as immunity-related genes, and may also depend on the genetic differences between breeding partners. We recorded breeding success of individuals and breeding pairs over 20 years to evaluate the relationships between reproductive success and both neutral genetic variation (using 7,830 single nucleotide polymorphisms) and functional variation (four toll-like receptor [TLRs] loci) with reproductive success in thick-billed murres (Uria lomvia). Individual genetic diversity (both neutral and functional) was unrelated to reproductive success, but surprisingly, successful multi-year reproductive success decreased with the genetic difference between breeding partners at TLR1Lb. This result may be due to an advantage of specific alleles at TLR1Lb. This study is one of few addressing both individual genetic variation and genetic similarity between mates at both neutral and functional variation in a long-lived bird.

The ability to assign biological samples to source populations based on genetic variation with high accuracy and precision is important for numerous applications from ecological studies through wildlife conservation to epidemiology. However, population assignment when genetic differentiation is low is challenging, and methods to address this problem are lacking. The application of artificial neural networks to population assignment using genomic data is highly promising. Here we present popfinder: a new, easy to use Python-based artificial neural network pipeline for genetic population assignment. We tested popfinder both with simulated genetic data from populations connected by varying levels of gene flow, and with reduced-representation sequence data for three species of seabirds with weak to no population genetic structure. Popfinder was able to assign individuals to their source populations with high accuracy, precision and recall in most cases, including both simulated and empirical datasets, except in the weakest empirical population structure dataset, where the comparator programs also performed poorly. Compared to other available software, popfinder was slower on the simulated data sets due to hyperparameter tuning and the fact that it does not reduce the dimensionality of the data set; however, all programs ran in seconds on empirical data sets. Additionally, popfinder provides a perturbation ranking method to help develop optimized SNP panels for genetic population assignment, and is designed to be user-friendly. Finally, we caution users of all assignment programs to watch both for leakage of data during model training, and for unequal detection probabilities.

The relative contributions of past and present evolutionary processes in shaping population genetic differentiation can be difficult to ascertain, especially in highly mobile animals. The Northern Gannet (Morus bassanus; hereafter, gannet) is a migratory colonial seabird that is widely distributed across the North Atlantic Ocean. Despite strong dispersal abilities, decades of banding and tracking studies indicate that the North Atlantic is a barrier for seasonal migration of gannets: gannets breeding in North America winter along the southeastern coast of USA and Mexico, while European breeders winter along the western European and African coasts. However, telemetry recently revealed that some gannets migrate across the ocean, suggesting that trans-Atlantic gene flow is possible. We investigated patterns of genomic variation among gannets from 12 colonies across the species’ range using double digest restriction-site associated sequencing (ddRADseq). Indices of genetic differentiation, principal component analysis, a Bayesian clustering method, and discriminant analysis of principal components all indicated that gannets breeding in North America versus Europe differ genetically, in accordance with segregation at both breeding and non-breeding areas. However, Bayesian assignment methods indicated that low, unidirectional introgression occurs from Europe into North America, suggesting that the North Atlantic is a semi-permeable barrier to gene flow in gannets. Evolutionary modeling suggested that the two genetic populations originated in separate refugia during the Pleistocene and underwent secondary contact during the Holocene. These results are consistent with results of previous studies and provide direct evidence that seasonal migratory behaviour can influence population genetic structure in a highly mobile organism.

Climate change poses a significant threat to Arctic ecosystems. Evaluation of genetic diversity within and differentiation among populations is needed to effectively conserve Arctic species and ensure genetic variation is appropriately managed. This research examined population genetic structure in Larus hyperboreus (Glaucous Gull), a circumpolar Arctic species that is declining in parts of its range. Population genetic information is needed to help delineate management units, including information on genetic differences among related species, among subspecies (currently distinguished by subtle morphometric and plumage differences), and among colonies in North America. We conducted double-digest restriction site-associated DNA sequencing for 62 L. hyperboreus, 18 L. argentatus smithsonianus (American Herring Gull), 6 L. a. argentatus (European Herring Gull), and 15 L. glaucescens (Glaucous-winged Gull) sampled across the Canadian and European Arctic. Interspecific analyses using 2,145 loci were unable to distinguish members of this species complex. Despite the geographic distance among sampling locations, molecular assignments and principal coordinates analyses based on 621 loci uncovered only weak population genetic differentiation among sampled European and Canadian colonies of L. hyperboreus. As L. hyperboreus occupying the eastern Canadian Arctic appear to be acting as a single panmictic population, conservation plans that protect Arctic habitat may help slow or reverse population declines. Proactive conservation strategies will benefit both L. hyperboreus and associated coastal Arctic ecosystems.