Genetic variation of the St. Lawrence beluga whale population assessed by DNA fingerprinting

Pathologic Findings and Trends in Mortality in the Beluga (Delphinapterus leucas) Population of the St Lawrence Estuary, Quebec, Canada, From 1983 to 2012

An isolated population of beluga (Delphinapterus leucas) inhabits the St Lawrence Estuary, Quebec, Canada. This population has failed to recover despite the prohibition of hunting >30 years ago, suggesting the presence of other limiting factors. The authors summarize the reported causes of death and propose risk factors to explain the lack of recovery of this population. From 1983 to 2012, a total of 472 beluga were found stranded. Complete necropsies were carried out on 222 beluga, including 178 adults, 25 juveniles, and 19 newborn calves. Infectious diseases, the most prevalent cause of mortality in this population, accounted for the death of one-third of all beluga (32%). Verminous pneumonia was the cause of mortality of 13 juvenile beluga (52% of juvenile beluga). A total of 39 malignant neoplasms, diagnosed in 35 beluga, caused the death of 31 beluga (20% of beluga >19 years old). Median age at diagnosis of cancer was 48 years (range, 30-61 years). Dystocia and postpartum complications were the cause of death in 18 beluga, accounting for 19% of the females >19 years old examined. The occurrence of parturition-associated complications, as well as mortality of calves <1 year old, have increased recently in this population and may be the probable cause of the recent decrease in the size of this population. One of the hypotheses proposed to explain the unusually high occurrence of some of the pathologic conditions observed in this population is chronic exposure to environmental contaminants.

Nucleotide sequence of the p53 cDNA of beluga whale (Delphinapterus leucas)

The cDNA (DNA complementary to RNA) of the p53 gene of the beluga whale (Delphinapterus leucas) was sequenced by the method of 5'- and 3'-rapid amplification of cDNA ends (RACE) with the cDNA made for the RNA obtained from fresh peripheral blood leukocytes isolated from two animals. Primers for the RACE method were synthesized based on the sequence of the DNA of beluga whale corresponding to exon 5 of the human p53 gene, which was determined after amplification of the DNA isolated from the liver from a beluga whale by using a pair of primers for the human sequence. The sequenced cDNA had a 2150-nucleotide length and contained the whole region corresponding to human exons 1 through 11. The reading frame was 1164 bp (base pair) long and began in exon 2 and ended in exon 11, coding for a 387-amino acid protein. The nucleotide sequence of the reading frame showed high similarity over 85% with pig, sheep, cow, and human genes. The similarities with the former two animals at the amino acid level were also more than 85%. Lower similarity of the beluga whale p53 gene was also found with those of lower tetrapods, fish and invertebrates.

Post-bottleneck genetic diversity of elephant populations in South Africa, revealed using microsatellite analysis

Widespread hunting had fragmented and severely reduced elephant populations in South Africa by 1900. Elephant numbers increased during the 1900s, although rates of recovery of individual populations varied. The Kruger National Park elephant population increased rapidly, to more than 6000 by 1967, with recruitment boosted by immigration from Mozambique. The Addo Elephant National Park population was reduced to 11 elephants in 1931 and remains relatively small (n = 325). Loss of genetic variation is expected to occur whenever a population goes through a bottleneck, especially when post-bottleneck recovery is slow. Variation at nine polymorphic microsatellite loci was analysed for Kruger and Addo elephants, as well as museum specimens of Addo elephants shot prior to the population bottleneck. Significantly reduced genetic variation and heterozygosity were observed in Addo in comparison to Kruger (mean alleles/locus and H(E): Addo 1.89, 0.18; Kruger 3.89, 0.44). Two alleles not present in the current Addo population were observed in the museum specimens. Addo elephants represent a genetic subset of the Kruger population, with high levels of genetic differentiation resulting from rapid genetic drift. The Kruger population is low in genetic diversity in comparison to East African elephants, confirming this population also suffered an appreciable bottleneck.

Sex-biased dispersal and a density-independent mating system in the Australian brushtail possum, as revealed by minisatellite DNA profiling

Natal dispersal can have important effects on mammal population structure and dynamics following a local population crash. Such dispersal is of practical importance when applied to the control of pest species because dispersal may significantly, and undesirably, reduce the population recovery time following a control operation. The relative dispersal rate of the sexes is also critical because that too will affect the rate of population increase. Here, we describe a field experiment in which we reduce the density of two populations of the Australian brushtail possum, and use genetic similarity, as estimated by minisatellite DNA profiles, to investigate dispersal in the original (undisturbed) and recovering populations. Our results show that the genetic similarity within the undisturbed populations was lower between males than between females. Conversely, the genetic similarities between males and females in the two recovering populations were not significantly different, while relatedness among males was significantly higher in the recovering populations when compared with those in the pre-removal populations. These data indicate two important characteristics of dispersal in possums: (i) that dispersal in established populations is sex biased towards males; and (ii) that within the first 3 years following population control, 'the vacuum effect', whereby individuals from areas adjacent to a control area expand their home range and invade the depopulated area, is the most important factor in the re-colonization process for possums. We found no evidence that the mating system, which is polygynous, varied when the density was markedly reduced. These results indicate that drastic reductions in population density by conventional control will not affect the rate of spread of biological control agents that rely on sexual transmission for dissemination.

DNA fingerprinting data and the analysis of population genetic structure by comparing band-sharing patterns

Genetic isolation among populations can be effectively investigated by multilocus DNA fingerprinting. If populations have diverged, it is expected that the mean proportion of bands shared by individuals from the same population, Bw, exceeds the corresponding mean, Bb, calculated from pairs of individuals from distinct populations. A problem arises in deciding whether any difference between Bw and Bb is statistically significant. In fact, any two band-sharing data (bij), contributing to Bw or Bb, are not independent if they share a common individual (like bij and bjl). This prevents a correct application of parametric tests, such as the Student's t-test. Recently, a modification of this test has been proposed that should avoid the independence problem. Using a large number of samples of fingerprints, simulated from an appropriate 'genetic' model, under a wide range of conditions, we compared the performances of the Student's t-test, the modified t-test and five new permutation tests, where individuals, rather than bij values, are permuted. We found that: (i) the Student's t-test can be very permissive, rejecting too often the null hypothesis when true, but is correct or conservative in certain cases; (ii) the modified t-test is extremely conservative when the null hypothesis is true and very inefficient otherwise; (iii) all five permutation tests are strictly correct, provided that individuals are ordered randomly on gels; and (iv) in this case, the permutation tests are equally efficient, and are not inferior to the Student's t-test when the latter is approximately correct and provides a fair benchmark.

Allelic and haplotype variation of major histocompatibility complex class II DRB1 and DQB loci in the St Lawrence beluga (Delphinapterus leucas)

In order to assess levels of major histocompatibility complex (Mhc) variation within the St Lawrence beluga (Delphinapterus leucas) the variation at the beluga Mhc DRB1 class II locus was assessed by single-strand conformation polymorphism (SSCP) analysis of the peptide-binding region for 313 whales collected from 13 sampling locations across North America. In addition, samples from west Greenland and the St Lawrence were also typed at the DQB locus, allowing comparison to a previous study and assessment of linkage disequilibrium of alleles at the two loci. Comparisons of DRB1 and DQB allele frequencies among all sampling locations indicated genetic structure (alpha < 0.005). Most of this structure resulted from differences between the different wintering groups. Significant genetic structure (alpha = 0.05) exists among each pair of the following groups at both the DRB1 and DQB loci; St Lawrence, Hudson Strait, Bering Sea, Cunningham Inlet, and Davis Strait (minus Cunningham Inlet), except the St Lawrence and Hudson Strait for the DQB locus. In the St Lawrence population, six of the eight DRB1 alleles are present representing all five known allelic lineages. Evidence of linkage disequilibrium between the DRB1 and DQB is present in two sampling locations, the St Lawrence and Nuussuaq (alpha = 0.05). Analysis of probable DRB1-DQB haplotypes among groups of beluga suggests a haplotype reduction in the St Lawrence.

Inbreeding of bottlenecked butterfly populations. Estimation using the likelihood of changes in marker allele frequencies

Polymorphic enzyme and minisatellite loci were used to estimate the degree of inbreeding in experimentally bottlenecked populations of the butterfly, Bicyclus anynana (Satyridae), three generations after founding events of 2, 6, 20, or 300 individuals, each bottleneck size being replicated at least four times. Heterozygosity fell more than expected, though not significantly so, but this traditional measure of the degree of inbreeding did not make full use of the information from genetic markers. It proved more informative to estimate directly the probability distribution of a measure of inbreeding, sigma2, the variance in the number of descendants left per gene. In all bottlenecked lines, sigma2 was significantly larger than in control lines (300 founders). We demonstrate that this excess inbreeding was brought about both by an increase in the variance of reproductive success of individuals, but also by another process. We argue that in bottlenecked lines linkage disequilibrium generated by the small number of haplotypes passing through the bottleneck resulted in hitchhiking of particular marker alleles with those haplotypes favored by selection. In control lines, linkage disequilibrium was minimal. Our result, indicating more inbreeding than expected from demographic parameters, contrasts with the findings of previous (Drosophila) experiments in which the decline in observed heterozygosity was slower than expected and attributed to associative overdominance. The different outcomes may both be explained as a consequence of linkage disequilibrium under different regimes of inbreeding. The likelihood-based method to estimate inbreeding should be of wide applicability. It was, for example, able to resolve small differences in sigma2 among replicate lines within bottleneck-size treatments, which could be related to the observed variation in reproductive viability.

DNA fingerprinting data and the problem of non-independence among pairwise comparisons

Multilocus DNA fingerprinting is commonly used to assess genetic similarity within and between geographically disjunct populations. Typically, the proportion of DNA fingerprinting bands shared between two individuals (SXY) is calculated for all possible pairwise comparisons and the resulting data analysed parametrically to test differences in mean band-sharing among groups. The degree to which covariation among interdependent SXY values (S(ab)-Sbc) biases the analyses is often unknown. Here, we assess the extent of covariation in four DNA fingerprinting studies and evaluate the effectiveness of two corrective procedures, a permutation test and a subsampling routine using only independent pairwise comparisons drawn without replacement from the overall data. Covariation among interdependent SXY values was significantly greater than zero in every data set examined, including those from a bee, a rodent, and two passerine birds. Permutation tests did not correct for interdependence and yielded significance values nearly identical to those derived from uncorrected parametric procedures. In contrast, the subsampling procedure yielded corrected estimates of the standard error that were two to four times larger than those derived parametrically. As a result, comparisons that were significant using parametric tests were either non-significant or only marginally significant with the subsampling routine. We conclude that interdependence among SXY values poses a substantial obstacle to hypothesis testing that must be addressed in future studies.

Helminths of an endangered population of belugas, Delphinapterus leucas, in the St. Lawrence estuary, Canada

Helminths were identified in 38 belugas, Delphinapterus leucas, stranded in the St. Lawrence estuary and Gulf of St. Lawrence during 1984–1993. These helminth species were Anisakis simplex, Contracaecinea sp., Pseudoterranova sp., Stenurus arctomarinus, Pharurus pallasii, Halocercus taurica (new host record), Halocercus monoceris (new host record), Hadwenius seymouri, Diphyllobothrium sp., and Bolbosoma sp. (new host record). Of 21 helminths previously reported from populations of belugas worldwide, 7 were found in the St. Lawrence population. Lungworms, such as Halocercus monoceris, may prove useful in identification of beluga populations in the Arctic and may also be an important cause of morbidity and mortality of calves.

Pathology and toxicology of beluga whales from the St. Lawrence Estuary, Quebec, Canada. Past, present and future

An indigenous population of 450-500 beluga whales (Delphinapterus leucas) inhabiting the St. Lawrence Estuary has been exposed chronically for more than 50 years to a complex mixture of industrial pollutants including organochlorinated compounds (OC), polycyclic aromatic hydrocarbons (PAH) and heavy metals. From 1983 to 1990, we have necropsied 45 well preserved carcasses out of a total of 120 beluga whales reported dead over this period. Of these 45 animals, nine were affected by 10 malignant neoplasms. Fifteen animals (33%) were affected by pneumonia. Milk production was compromised in eight of 17 mature females (41%), by inflammatory changes (seven animals) and cancer (one animal) which affected the mammary glands. Opportunistic bacteria were found in pure culture, and/or in significant amounts in at least two organs in 20 belugas (44%). The concentrations of both total PCBs and highly chlorinated PCB congeners were much higher in St. Lawrence animals than in Arctic beluga whales. OC-induced immunosuppression has been repeatedly demonstrated in a wide variety of animal species. Therefore, it is probable that the immune functions of St. Lawrence beluga whales are impaired. Benzo[a]pyrene adducts were detected in 10 of the 11 St. Lawrence beluga whales of which tissues (six livers, 10/11 brains) were analyzed by a method based on HPLC. No such adducts were found in four Arctic animals. Since benzo[alpha]pyrene is one of the most potent chemical carcinogens known to man, these compounds might be responsible for some of the cancers observed in that population. Overall, our findings contrast vividly with those of others who found that cancers are exceedingly rare in free-ranging odontocete populations and that the major causes for mortalities in these populations are bacteria, parasites, and trauma.