Mitochondrial DNA reveals secondary contact in Japanese harbour seals, the southernmost population in the western Pacific.

In this study, we used relatively large number of samples (n = 178) and control region of mtDNA (454bp) to clearify the divergence history of Japanese harbour seals (Phoca vitulina stejnegeri) and phylogenetic relationship between the seals in Japan and other countries. Our results suggested that Japanese harbour seals possibly consisted of more than two lineages and secondary contact of populations after a long isolation. Furthermore, one of the lineage was made only by Japanese harbour seals (Group P1). The proportion of Group P1 was the highest at the South West and gradually decreased towards the North East of Hokkaido, Japan. On the other hand, the haplotypes do not belonged to Group P1 showed close relationship to the seals in the North Pacific. Based on the fossil record of harbour seal in Japan and the range of sea ice during the Last Glacial Maximum (LGM), Group P1 might have entered Japan before the LGM and became isolated due to the geographical boundary, and gradually extended its range from the South West towards the North East of Hokkaido after the disappearance of the sea ice, while the seals which are not in Group P1 immigrated into Japan from the North Pacific.

Temporal and spatial variation in harbor seal (Phoca vitulina L.) roar calls from southern Scandinavia.

Male harbor seals gather around breeding sites for competitive mating displays. Here, they produce underwater vocalizations possibly to attract females and/or scare off other males. These calls offer prospects for passive acoustic monitoring. Acoustic monitoring requires a good understanding of natural variation in calling behavior both temporally and among geographically separate sites. Such variation in call structure and calling patterns were studied in harbor seal vocalizations recorded at three locations in Danish and Swedish waters. There was a strong seasonality in the calls from end of June to early August. Vocalizations at two locations followed a diel pattern, with an activity peak at night. Recordings from one location also showed a peak in call rate at high tide. Large geographic variations were obvious in the total duration of the so-called roar call, the duration of the most prominent part of the call (the roar burst), and of percentage of energy in roar burst. A similarly large variation was also found when comparing the recordings from two consecutive years at the same site. Thus, great care must be taken to separate variation attributable to recording conditions from genuine biological differences when comparing harbor seal roars among recording sites and between years.

Classification of underwater vocalizations of wild spotted seals (Phoca largha) in Liaodong Bay, China.

Underwater vocalizations were recorded and classified from wild spotted seals (Phoca largha) in Liaodong Bay, China. The spotted seals exhibited an extensive underwater vocal repertoire but with limited complexity. Four major call types, representing 77.8% of all calls recorded, were identified using multivariate analyses of ten acoustic parameters; knock, growl, drum, and sweep. The calls were relatively brief (12-270 ms, mean of -10 dB duration) pulsating sounds of low-frequency (peak frequency <600 Hz) and narrow bandwidth (169-232 Hz, mean of -3 dB bandwidth; 237-435 Hz, mean of -6 dB bandwidth). Frequency variables (-3/-6 dB frequency bandwidth, center frequency, and top three peak frequencies) were the primary descriptors used to differentiate the call types. Comparing the spotted seal underwater vocalizations with those of the closely related Pacific harbor seal (Phoca vitulina richardii) indicated that the two species use similar bandwidths and peak frequencies but spotted seal calls were generally shorter. Knowledge of underwater vocalizations of wild spotted seals is important for understanding the species behavior and for planning future acoustic surveys of its distribution and occurrence.

Source levels and call parameters of harbor seal breeding vocalizations near a terrestrial haulout site in Glacier Bay National Park and Preserve.

Source levels of harbor seal breeding vocalizations were estimated using a three-element planar hydrophone array near the Beardslee Islands in Glacier Bay National Park and Preserve, Alaska. The average source level for these calls was 144 dBRMS re 1 µPa at 1 m in the 40-500 Hz frequency band. Source level estimates ranged from 129 to 149 dBRMS re 1 µPa. Four call parameters, including minimum frequency, peak frequency, total duration, and pulse duration, were also measured. These measurements indicated that breeding vocalizations of harbor seals near the Beardslee Islands of Glacier Bay National Park are similar in duration (average total duration: 4.8 s, average pulse duration: 3.0 s) to previously reported values from other populations, but are 170-220 Hz lower in average minimum frequency (78 Hz).

wisepair: a computer program for individual matching in genetic tracking studies.

Individual-based data sets tracking organisms over space and time are fundamental to answering broad questions in ecology and evolution. A 'permanent' genetic tag circumvents a need to invasively mark or tag animals, especially if there are little phenotypic differences among individuals. However, genetic tracking of individuals does not come without its limits; correctly matching genotypes and error rates associated with laboratory work can make it difficult to parse out matched individuals. In addition, defining a sampling design that effectively matches individuals in the wild can be a challenge for researchers. Here, we combine the two objectives of defining sampling design and reducing genotyping error through an efficient Python-based computer-modelling program, wisepair. We describe the methods used to develop the computer program and assess its effectiveness through three empirical data sets, with and without reference genotypes. Our results show that wisepair outperformed similar genotype matching programs using previously published from reference genotype data of diurnal poison frogs (Allobates femoralis) and without-reference (faecal) genotype sample data sets of harbour seals (Phoca vitulina) and Eurasian otters (Lutra lutra). In addition, due to limited sampling effort in the harbour seal data, we present optimal sampling designs for future projects. wisepair allows for minimal sacrifice in the available methods as it incorporates sample rerun error data, allelic pairwise comparisons and probabilistic simulations to determine matching thresholds. Our program is the lone tool available to researchers to define parameters a priori for genetic tracking studies.

Sequence variation and gene duplication at the MHC DRB loci of the spotted seal Phoca largha.

The major histocompatibility complex (MHC) is one of the most important genetic systems associated with resistance to infectious diseases in vertebrates. The spotted seal (Phoca largha) is one of the most endangered species in China. In this study, we present the first step in the molecular characterization of a DRB-like locus in the spotted seal by analyzing the nucleotide sequence of the polymorphic exon 2 segments, a 288-nucleotide sequence. By examining the segment from a group of 41 individuals, 28 alleles were identified. No deletion, insertion, or exceptional stop codon was detected, suggesting that these alleles could be functional in vivo. The nucleotide and amino acid sequences of the segment both showed a relatively high level of similarity (nucleotides 97%; amino acids 98%) to those of Meles meles and Zalophus californianus. The high level of spotted seal MHC-DRB polymorphism revealed in the present study has not been reported for the Phocidae and could be a consequence of the small spotted seal population adapting to the Bohai Sea, which probably has a relatively high level of pathogens.

Canine distemper virus diversity in Lake Baikal seal (Phoca sibirica) population.

Morbillivirus epizootics in marine mammals have been found in a variety of marine mammal species throughout the world over the past 20 years. The virus epizootic which resulted in significant mortality of Siberian seals (Phoca sibirica) in Lake Baikal during 1987-1988 was caused by the canine distemper virus (CDV). In our previous papers we provided evidence that the CDV similar to strain, identified in 1988, continued to circulate in Lake Baikal seals after 1988. The aim of this study was an up to date detection of CDV in Baikal seals and an evaluation of the genetic diversity of Baikal seal CDVs in comparison with other virus isolates and strains available in the GenBank on the basis of nucleotide sequence analysis of the phosphoprotein gene fragment. The majority of CDVs recovered from 1992 till 2007 were found to be similar to the one responsible for the epizootic of Lake Baikal seals. Phylogenetic analysis revealed that more than one genotype of CDV was circulating in Lake Baikal seals after the epizootic of 1987-1988.