Sequence Diversity and Differences at the Highly Duplicated MHC-I Gene Reflect Viral Susceptibility in Sympatric Pinniped Species.

Differences in disease susceptibility among species can result from rapid host-pathogen coevolution and differences in host species ecology that affect the strength and direction of natural selection. Among 2 sympatric pinniped species that differ in sociality and putative disease exposure, we investigate observed differences in susceptibility through an analysis of a highly variable, duplicated gene family involved in the vertebrate immune response. Using high-throughput amplicon sequencing, we characterize diversity at the 2 exons that encode the peptide binding region of the major histocompatibility complex class I (MHC-I) gene in harbor (N = 60) and gray (N = 90) seal populations from the Northwest Atlantic. Across species, we identified 106 full-length exon 2 and 103 exon 3 sequence variants and a minimum of 11 duplicated MHC-I loci. The sequence variants clustered in 15 supertypes defined by the physiochemical properties of the peptide binding region, including a putatively novel Northwest Atlantic MHC-I diversity sublineage. Trans-species polymorphisms, dN/dS ratios, and evidence of gene conversion among supertypes are consistent with balancing selection acting on this gene. High functional redundancy suggests particularly strong selection among gray seals at the novel Northwest Atlantic MHC-I diversity sublineage. At exon 2, harbor seals had a significantly greater number of variants per individual than gray seals, but fewer supertypes. Supertype richness and private supertypes are hypothesized to contribute to observed differences in disease resistance between species, as consistently, across the North Atlantic and many disease outbreaks, gray seals appear to be more resistant to respiratory viruses than harbor seals.

Genomic signatures of population bottleneck and recovery in Northwest Atlantic pinnipeds.

Population increases over the past several decades provide natural settings in which to study the evolutionary processes that occur during bottleneck, growth, and spatial expansion. We used parallel natural experiments of historical decline and subsequent recovery in two sympatric pinniped species in the Northwest Atlantic, the gray seal (Halichoerus grypus atlantica) and harbor seal (Phoca vitulina vitulina), to study the impact of recent demographic change in genomic diversity. Using restriction site-associated DNA sequencing, we assessed genomic diversity at over 8,700 polymorphic gray seal loci and 3,700 polymorphic harbor seal loci in samples from multiple cohorts collected throughout recovery over the past half-century. Despite significant differences in the degree of genetic diversity assessed in the two species, we found signatures of historical bottlenecks in the contemporary genomes of both gray and harbor seals. We evaluated temporal trends in diversity across cohorts, as well as compared samples from sites at both the center and edge of a recent gray seal range expansion, but found no significant change in genomewide diversity following recovery. We did, however, find that the variance and degree of allele frequency change measured over the past several decades were significantly different from neutral expectations of drift under population growth. These two cases of well-described demographic history provide opportunities for critical evaluation of current approaches to simulating and understanding the genetic effects of historical demographic change in natural populations.

Assessing the disturbance potential of small unoccupied aircraft systems (UAS) on gray seals (Halichoerus grypus) at breeding colonies in Nova Scotia, Canada.

The use of small unoccupied aircraft systems (UAS) for ecological studies and wildlife population assessments is increasing. These methods can provide significant benefits in terms of costs and reductions in human risk, but little is known if UAS-based approaches cause disturbance of animals during operations. To address this knowledge gap, we conducted a series of UAS flights at gray seal breeding colonies on Hay and Saddle Islands in Nova Scotia, Canada. Using a small fixed-wing UAS, we assessed both immediate and short-term effects of surveys using sequential image analysis and between-flight seal counts in ten, 50 m2 random quadrats at each colony. Counts of adult gray seals and young-of-the-year animals between first and second flights revealed no changes in abundance in quadrats (matched pair t-test p > 0.69) and slopes approaching 1 for linear regression comparisons (r2 > 0.80). Sequential image analysis revealed no changes in orientation or posture of imaged animals. We also assessed the acoustic properties of the small UAS in relation to low ambient noise conditions using sound equivalent level (Leq) measurements with a calibrated U-MIK 1 and a 1/3 octave band soundscape approach. The results of Leq measurements indicate that small fixed-wing UAS are quiet, with most energy above 160 Hz, and that levels across 1/3 octave bands do not greatly exceed ambient acoustic measurements in a quiet field during operations at standard survey altitudes. As such, this platform is unlikely to acoustically disturb gray seals at breeding colonies during population surveys. The results of the present study indicate that the effects of small fixed-wing UAS on gray seals at breeding colonies are negligible, and that fixed-wing UAS-based approaches should be considered amongst best practices for assessing gray seal colonies.

Diving heart rate development in postnatal harbour seals, Phoca vitulina.

Harbour seals, Phoca vitulina, dive from birth, providing a means of mapping the development of the diving response, and so our objective was to investigate the postpartum development of diving bradycardia. The study was conducted May-July 2000 and 2001 in the St. Lawrence River Estuary (48 degrees 41'N, 68 degrees 01'W). Both depth and heart rate (HR) were remotely recorded during 86,931 dives (ages 2-42 d, n = 15) and only depth for an additional 20,300 dives (combined data covered newborn to 60 d, n = 20). The mean dive depth and mean dive durations were conservative during nursing (2.1 +/- 0.1 m and 0.57 +/- 0.01 min, range = 0-30.9 m and 0-5.9 min, respectively). The HR of neonatal pups during submersion was bimodal, but as days passed, the milder of the two diving HRs disappeared from their diving HR record. By 15 d of age, most of the dive time was spent at the lower diving bradycardia rate. Additionally, this study shows that pups are born with the ability to maintain the lower, more fully developed dive bradycardia during focused diving but do not do so during shorter routine dives.

Developmental changes in cardiorespiratory patterns associated with terrestrial apnoeas in harbour seal pups.

During the nursing period seals undergo several physiological and behavioural changes. A key component of development is increased cardiorespiratory control, fundamental for breath-holding and thus diving. This study focused on the ontogenetic changes in cardiac responses to respiration in quietly resting, pre-weaned harbour seal pups (Phoca vitulina). During periods of quiet rest, breathing became episodic, eupnoea interspersed with periods of apnoea. Little change was observed in respiration (approximately 35 breaths min(-1)) and eupnoeic heart rate (approximately 160 beats min(-1)) throughout the nursing period. However, apnoea duration increased (from approximately 20 to 40 s), while apnoeic heart rate decreased with age (from approximately 150 to 90 beats min(-1)). The observed decline in apnoeic heart rate resulted from an increase in cardiorespiratory control as pups approached weaning, evident by the ability to maintain a lower heart rate more consistently. Similar changes in cardiorespiratory patterns have been reported for elephant and Weddell seals. Due to the early onset of independent foraging, however, the rate of cardiorespiratory control development was more rapid in harbour seals. Our findings suggest that by 1 month of age, harbour seal pups possess the cardiorespiratory control necessary to sustain long-duration apnoeas, fundamental for proficient diving and successful foraging upon weaning.