Robert Ea Stewart

Demographic inferences using short-read genomic data in an approximate Bayesian computation framework: in silico evaluation of power, biases and proof of concept in Atlantic walrus

Approximate Bayesian computation (ABC) is a powerful tool for model‐based inference of demographic histories from large genetic data sets. For most organisms, its implementation has been hampered by the lack of sufficient genetic data. Genotyping‐by‐sequencing (GBS) provides cheap genome‐scale data to fill this gap, but its potential has not fully been exploited. Here, we explored power, precision and biases of a coalescent‐based ABC approach where GBS data were modelled with either a population mutation parameter (θ) or a fixed site (FS) approach, allowing single or several segregating sites per locus. With simulated data ranging from 500 to 50 000 loci, a variety of demographic models could be reliably inferred across a range of timescales and migration scenarios. Posterior estimates were informative with 1000 loci for migration and split time in simple population divergence models. In more complex models, posterior distributions were wide and almost reverted to the uninformative prior even with 50 000 loci. ABC parameter estimates, however, were generally more accurate than an alternative composite‐likelihood method. Bottleneck scenarios proved particularly difficult, and only recent bottlenecks without recovery could be reliably detected and dated. Notably, minor‐allele‐frequency filters – usual practice for GBS data – negatively affected nearly all estimates. With this in mind, we used a combination of FS and θ approaches on empirical GBS data generated from the Atlantic walrus (Odobenus rosmarus rosmarus), collectively providing support for a population split before the last glacial maximum followed by asymmetrical migration and a high Arctic bottleneck. Overall, this study evaluates the potential and limitations of GBS data in an ABC‐coalescence framework and proposes a best‐practice approach.

Microsatellite assessment of walrus ( Odobenus rosmarus rosmarus ) stocks in Canada

Walruses in Canada are currently subdivided into seven stocks based on summering areas; Western Jones Sound (WJS), Baffin Bay (BB), Penny Strait-Lancaster Sound (PS-LS), North Foxe Basin (N-FB), Central Foxe Basin (C-FB), Hudson Bay Davis Strait (HB-DS) and Southern and Eastern Hudson Bay (SE-HB). In this study, walrus were sampled from six of the seven stocks (SE-HB samples were not available) and genotyped at 10 microsatellite loci. All stocks were genetically diverse (average heterozygosity of 0.58) with no evidence of inbreeding (average F IS of 0.03). We detected significant genetic differentiation among the stocks and a pattern of genetic spatial autocorrelation that suggests a moderate effect of geographic distance on gene flow among stocks. Bayesian clustering suggested the six recognized stocks were elements of two larger genetic clusters - a northern Arctic population (containing BB, WJS, and PS-LS stocks) and a central Arctic population (containing C-FB, N-FB, and HB-DS stocks). These populations are moderately differentiated ( F ST = 0.07), but based on evidence of contemporary movement from assignment tests, are not completely isolated. There was support for maintaining the WJS stock and a combined BB+PS-LS stock, although the latter conclusion is based on a small sample size. Similarly, there was some evidence suggesting separation of the Foxe Basin stocks from the HB-DS but not the N-FB from the C-FB stock. However, given that there are morphological and chemical differences between N-FB and C-FB stocks, there is currently insufficient evidence to support a revision of the current stock designations.

A genetic comparison of West Greenland and Baffin Island (Canada) walruses: Management implications

Until recently Atlantic walruses ( Odobenus rosmarus rosmarus ) have been subject to relatively intense exploitation in West Greenland. Animals in this stock have also been hunted in Nunavut/Canada. However, the demographic identity of these animals and their connection with walruses in neighbouring areas is poorly resolved, hampering the determination of sustainable harvest levels. It has been suggested that walruses in West Greenland are genetically linked with walruses at SE Baffin Island (Canada) where they are also hunted for subsistence purposes. To determine the relationship(s) between walruses in these areas we conducted a genetic analysis including recent samples from West Greenland, Southeast Baffin Island in western Davis Strait, Hudson Strait in Canada and Northwest Greenland in northern Baffin Bay. Seventeen microsatellite markers were applied to all samples. Walruses in West Greenland and at Southeast Baffin Island did not differ from each other and therefore may be regarded as belonging to the same stock. However, walruses in these two areas differed genetically from both Northwest Greenland and Hudson Strait walruses. These findings support (1) that there are subunits within the range of walruses in the Hudson Strait-Davis Strait-Baffin Bay region and (2) that walruses along E Baffin Island and W Greenland constitute a common population that receive some influx from Hudson Strait. Thus, sustainable catch levels in Southeast Baffin Island (Nunavut) and in West Greenland must be set in light of the finding that they belong to the same stock, which is exploited in these two areas. This requires Canadian-Greenlandic co-management of the W Greenland-SE Baffin Island walrus stock.

Movements of walruses ( Odobenus rosmarus ) between Central West Greenland and Southeast Baffin Island, 2005-2008

Between 2005 and 2008, 31 walruses were tagged with Argos satellite transmitters at their wintering grounds at Store Hellefiske Banke, Central West Greenland (N=23), and at their summering grounds off the coast of Southeast Baffin Island, Canada (N=8). Two male walruses moved along the Greenland coast from Store Hellefiske Banke north to Disko Banke, where contact was lost. Two other males went further north, up to the Upernavik area. Contact was lost with one of these tags, but the other animal travelled southward again and went towards SE Baffin Island. Eight of the tagged walruses moved between West Greenland and Baffin Island, demonstrating a connection between walruses at these sites. Walruses left the Store Hellefiske Banke during the period 7 April to 17 May and on average used 7 days to swim the 400 km across Davis Strait. The migration routes were quite similar; they travelled over the shallowest areas at the narrowest part of the strait. The timing of the spring dispersal and migration towards Canada was closely linked to the extent and timing of the retreat of the pack ice edge. One flipper tagged male that was marked off South Baffin Island was recovered in a hunt on Store Hellefiske Banke, documenting that the reverse migration also occurs. Off West Greenland satellite tagged walruses spent a lot of time around the Store Hellefiske Banke ( 55.0 o -56.5 o W), using this shallow area as feeding grounds irrespective of the ice cover in this area. Partial sexual segregation was observed. Despite a tendency in West Greenland for males to occur farther offshore, farther from the ice edge and at greater depths, only their preference for denser ice cover (64% ice cover) differed significantly (P=0.019) from the habitat preferences of females (52% ice cover). Coast dispersal was more condensed and the segregation between males and females was more pronounced during autumn along the Southeast Baffin Island. Females remained farther north (P<0.001) and farther east (P=0.006), and males were more often located offshore in areas with greater water depths (P=0.024). Males had also had larger home range than females during both seasons.

Abundance of Atlantic walrus in Western Nares Strait, Baffin Bay Stock, during summer

Atlantic walruses ( Odobenus rosmarus rosmarus ) belonging to the Baffin Bay subpopulation occur year round in the North Water polynya (NOW) between NW Greenland and eastern Ellesmere Island (Canada). They are hunted for subsistence purposes by residents of the Qaanaaq area (NW Greenland) bordering the NOW to the east and by Canadian Inuit at the entrance to Jones Sound in Nunavut. During the open-water period NW Greenland is virtually devoid of walruses which concentrate along eastern and southern Ellesmere Island at this time of the year. To determine the abundance of walruses in the NOW area, aerial surveys were conducted in August of 1999, 2008, and 2009. In July 2009, nine satellite-linked transmitters were deployed in nearby Kane Basin. Surveys on 9 and 20 August 2009 along eastern Ellesmere Island were the most extensive and were augmented with concomitant data on haul-out and at water surface activity from three (1 F, 2 M) of the nine tags that were still functioning. We therefore focus on the 2009 surveys. Walruses were observed on the ice and in water primarily in Buchanan Bay and Princess Marie Bay where the remaining functional tags were located. The Minimum Counted population (MCP) was 571 on 20 August. Adjusting the MCP of walruses on ice for those not hauled out, the estimate of abundance of walruses in the Baffin Bay stock was 1,251(CV=1.00, 95% CI = 1,226) when adjusted by the proportion of tags ‘dry’ at the time of the survey and 1,249 (CV=1.12, 95% CI = 1,370) when adjusted by the average time tags were dry. The surveys did not cover all potential walrus summering habitat along eastern Ellesmere Island and are negatively biased to an unknown degree.

A catch history for Atlantic walruses ( Odobenus rosmarus rosmarus ) in the eastern Canadian Arctic

Knowledge of changes in abundance of Atlantic walruses ( Odobenus rosmarus rosmarus ) in Canada is important for assessing their current population status. This catch history collates available data and assesses their value for modelling historical populations to inform population recovery and management. Pre-historical (archaeological), historical ( e.g., Hudson Bay Company journals) and modern catch records are reviewed over time by data source (whaler, land-based commercial, subsistence etc.) and biological population or management stock. Direct counts of walruses landed as well as estimates based on hunt products ( e.g. , hides, ivory) or descriptors ( e.g. , Peterhead boatloads) support a minimum landed catch of over 41,300 walruses in the eastern Canadian Arctic between 1820 and 2010. Little is known of Inuit catches prior to 1928, despite the importance of walruses to many Inuit groups for subsistence. Commercial hunting from the late 1500s to late 1700s extirpated the Atlantic walrus from Quebec and the Atlantic Provinces, but there was no commercial hunt for the species in the Canadian Arctic until ca. 1885. As the availability of bowhead whale ( Balaena mysticetus ) declined, whalers increasingly turned to hunting other species, including walruses. Modest numbers (max. 278/yr) were taken from the High Arctic population in the mid-1880s and large catches (up to 1400/yr) were often taken from the Central Arctic population from 1899 -1911, while the Foxe Basin stock (Central Arctic population) and Low Arctic population were largely ignored by commercial hunters. Land-based traders ( ca. 1895-1928) continued the commercial hunt until regulatory changes in 1928 reserved walruses for Inuit use. Since 1950, reported walrus catches have been declining despite a steady increase in the Inuit population. Effort data are needed to assess whether lower catches stem from declining hunter effort or decreased walrus abundance. The recent take of walruses by sport hunting has been small (n=141, 1995-2010), sporadic and local. These landed catch estimates indicate the minimum numbers of walruses removed but do not account for under-reporting or lost animals that were killed but were not secured. Unreported and lost animals may represent a significant fraction of the total removals and must be considered in any modelling exercise. The sources, quality and completeness of the catch data vary widely over time and space and between the different hunt types. This variability confounds interpretation and contributes to the uncertainty that needs to be incorporated into any modelling. The data on Inuit subsistence catches before ca. 1928 are particularly fragmentary and uncertain.

Use of Multiple Methods to Estimate Walrus ( Odobenus rosmarus rosmarus ) Abundance in the Penny Strait-Lancaster Sound and West Jones Sound Stocks, Canada

Surveys to estimate walrus abundance at terrestrial haulout sites in the Penny Strait-Lancaster Sound (PS-LS) and West Jones Sound (WJS) stocks were conducted in 1977 and 1998-2009. The Minimum Counted Population (MCP) was similar in 1977 (565) to recent years (557) for the PS-LS stock. The MCP for the WJS stock was higher in recent surveys (404) than in 1977 (290). Regression analysis of MCP and density (number of walrus divided by number of haulouts surveyed) showed no significant trends over time. We also calculated bounded count estimates for comparison. Finally, we used broad-scale behavioural data to estimate the proportion of the total stock that could be considered countable, to produce two adjusted estimates. We selected recent surveys with good coverage and ignored adjusted estimates that were lower than MCP. For the PS-LS stock, the adjusted MCP (with 95% CL) was 672 (575-768) and 727 (623-831) walrus in 2007 and 2009, respectively. For WJS, the best estimates were the adjusted MCP of 503 (473-534) in 2008 and the adjusted bounded count of 470 (297-1732) in 2009. While both stocks appear to have remained stable over three decades, differences in survey coverage and possible differences in walrus distribution make precise population estimation difficult.

Bomb dating, age validation and quality control of age determinations of monodontids and other marine mammals

Methods for confirming the accuracy of age determination methods are reasonably well established in fishes, but the millions of routine age determinations which take place every year require their own quality control protocols. In contrast, methods for ensuring accuracy in age determination of monodontids and other marine mammals are still being developed. Here we review the basis and application of bomb radiocarbon to marine mammal age validation, highlighting its value for providing unambiguous estimates of age for belugas and other long-lived animals which form growth bands. Bomb radiocarbon is particularly useful for marine mammals, given that the age of an individual animal can be determined to within ±1-3 years, as long as it was alive during the 1960s. However, ongoing age determinations require careful monitoring to ensure that age interpretations remain consistent across ages and through time. Quality control protocols using reference collections of ageing material, in conjunction with age bias plots and measures of precision, are capable of detecting virtually all of the systematic ageing errors that often occur once age determinations of an animal become routine.

Estimates of Minimum Population Size for Walrus near Southeast Baffin Island, Nunavut

To support management objectives in Canada and Greenland, joint research between the Department of Fisheries and Oceans and Greenland Institute of Natural Resources was begun in 2005. Direct counts were used to determine the Minimum Counted Population (MCP) in summer around SE Baffin Island. Aerial surveys examined the coast from roughly the Saddleback Island in northern Hudson Strait to Isabella Bay on eastern Baffin Island but concentrated on the area between Loks Land and Cape Dyer. The maximum count was obtained on 3–4 September 2007 during boat surveys. The MCP ranged from 716 (in 2006) to 1,056 (2007). Using the largest MCP adjusted with published maximum estimates of the proportion of walrus hauled out concurrently, we estimated 1,420 (95% CI: 1,219–1,622) walrus were present. In addition, four walrus had been fitted with satellite relayed data logger tags prior to the maximum counts in 2007. Using the simple proportion of ‘tags dry’ on 3 September to adjust counts on 3 and 4 September 2007 provided an estimate of 2,102 (CI = MCP-4,482). Using the proportion of time dry immediately preceding the survey to adjust the maximum count produced an estimate of 2,502 (CI = 1,660–3,345) walrus were present in Hoare Bay. We conclude approximately 2,100–2,500 walrus were present in Hoare Bay in late summer 2007. This number is a negatively biased estimator of the population of walrus around SE Baffin Island and in the Hudson Bay–Davis Strait stock as a whole. Broader survey coverage in a short period and more detailed information on the movement of walrus between Greenland and Canada and the summer dispersal of these animals within Canada are required to improve population estimates.

Inter-lab comparison of precision and recommended methods for age estimation of Florida manatee (Trichechus manatus latirostris) using growth layer groups in earbones

Manatees are routinely aged by counting Growth Layer Groups (GLGs) in periotic bones (earbones). Manatee carcasses recovered in Florida between 1974 and 2010 provided age-estimation material for three readers and formed the base for a retrospective analysis of aging precision (repeatability). All readers were in good agreement (high precision) with the greatest apparent source of variation being the result of earbone remodelling with increasing manatee age. Over the same period, methods of sample preparation and of determining a final age estimate changed. We examined the effects of altering methods on ease of reading GLGs and found no statistical differences. Accurate age estimates are an important component for effective management of the species and for better models of population trends and we summarize the currently recommended methods for estimating manatee ages using earbones.