Guidelines for genetic data analysis

The IWC Scientific Committee recently adopted guidelines for quality control of DNA data. Once data have been collected, the next step is to analyse the data and make inferences that are useful for addressing practical problems in conservation and management of cetaceans. This is a complex exercise, as numerous analyses are possible and users have a wide range of choices of software programs for implementing the analyses. This paper reviews the underlying issues, illustrates application of different types of genetic data analysis to two complex management problems (involving common minke whales and humpback whales), and concludes with a number of recommendations for best practices in the analysis of population genetic data. An extensive Appendix provides a detailed review and critique of most types of analyses that are used with population genetic data for cetaceans.Publisher PDFPeer reviewe

Assessment of genetic structure among eastern North Pacific gray whales on their feeding grounds

Although most eastern North Pacific (ENP) gray whales feed in the Bering, Beaufort, and Chukchi Seas during summer and fall, a small number of individuals, referred to as the Pacific Coast Feeding Group (PCFG), show intra- and interseasonal fidelity to feeding areas from northern California through southeastern Alaska. We used both mitochondrial DNA (mtDNA) and 12 microsatellite markers to assess whether stock structure exists among feeding grounds used by ENP gray whales. Significant mtDNA differentiation was found when samples representing the PCFG (n = 71) were compared with samples (n = 103) collected from animals feeding further north (Fₛₜ = 0.012, P = 0.0045). No significant nuclear differences were detected. These results indicate that matrilineal fidelity plays a role in creating structure among feeding grounds but suggests that individuals from different feeding areas may interbreed. Haplotype diversities were similar between strata (hₚCFG = 0.945, hₙₒᵣₜₕₑᵣₙ = 0.952), which, in combination with the low level of mtDNA differentiation identified, suggested that some immigration into the PCFG could be occurring. These results are important in evaluating the management of ENP gray whales, especially in light of the Makah Tribe’s proposal to resume whaling in an area of the Washington coast utilized by both PCFG and migrating whales

Summary from an international cancer seminar focused on human papillomavirus (HPV)-positive oropharynx cancer, convened by scientists at IARC and NCI

Cancer of the oropharynx has attracted considerable attention in recent years given: (1) an increasing incidence in selected populations over the past three decades; (2) the discovery of human papillomavirus (HPV) infection as the driver of the increase, as opposed to the traditional risk factors such as tobacco (smoking and chewing) and alcohol; and (3) the promise of new prevention and treatment strategies. As a result of such developments, the International Agency for Research on Cancer (IARC) and the US National Cancer Institute (NCI), convened the fourth Cancer Seminar meeting in November 2018 to focus on this topic. This report summarizes the proceedings: a review of recent science on the descriptive epidemiology, etiology, biology, genetics, early detection, pathology and treatment of HPV-positive oropharyngeal cancer, and the formulation of key research questions to be addressed

Human Papillomavirus Antibodies And Future Risk Of Anogenital Cancer: A Nested Case-control Study In The European Prospective Investigation Into Cancer And Nutrition Study

Purpose: Human papillomavirus (HPV) type 16 (HPV16) causes cancer at several anatomic sites. In the European Prospective Investigation Into Cancer and Nutrition study, HPV16 E6 seropositivity was present more than 10 years before oropharyngeal cancer diagnosis and was nearly absent in controls. The current study sought to evaluate the extent to which HPV16 E6 antibodies are present before diagnosis of anogenital cancers within the same cohort. Methods: Four hundred incident anogenital cancers (273 cervical, 24 anal, 67 vulvar, 12 vaginal, and 24 penile cancers) with prediagnostic blood samples (collected on average 3 and 8 years before diagnosis for cervix and noncervix cancers, respectively) and 718 matched controls were included. Plasma was analyzed for antibodies against HPV16 E6 and multiple other HPV proteins and genotypes and evaluated in relation to risk using unconditional logistic regression. Results: HPV16 E6 seropositivity was present in 29.2% of individuals (seven of 24 individuals) who later developed anal cancer compared with 0.6% of controls (four of 718 controls) who remained cancer free (odds ratio [OR], 75.9; 95% CI, 17.9 to 321). HPV16 E6 seropositivity was less common for cancers of the cervix (3.3%), vagina (8.3%), vulva (1.5%), and penis (8.3%). No associations were seen for non-type 16 HPV E6 antibodies, apart from anti-HPV58 E6 and anal cancer (OR, 6.8; 95% CI, 1.4 to 33.1). HPV16 E6 seropositivity tended to increase in blood samples drawn closer in time to cancer diagnosis. Conclusion: HPV16 E6 seropositivity is relatively common before diagnosis of anal cancer but rare for other HPV-related anogenital cancers

The population genetics of gray whales (Eschrichtius robustus) in the North Pacific

Within the North Pacific, gray whales (Eschrichtius robustus) are recognized as distinct eastern and western populations. Although both populations were severely reduced by whaling, the eastern population is generally considered to have recovered while the western population has remained highly depleted. This study expanded on previous work supporting differentiation between eastern and western populations using mtDNA and utilized a panel of 13 microsatellite loci to provide additional insight into the population structure of gray whales. Comparison of microsatellite allele frequencies indicated that eastern and western populations are genetically distinct. Although highly statistically significant, the level of nuclear differentiation between the two populations was relatively low, and the results of sex-specific analyses and assignment testing suggested that some degree of male- biased dispersal may occur between populations. Within the set of samples collected from animals on the primary western feeding ground, relatedness analyses revealed that, consistent with field observations, the fidelity of females and their offspring to this area have been important in shaping the structure of the population. Furthermore, analysis of the paternity of animals first identified as calves, with known and sampled mothers, in the western population between 1995 and 2007 identified 18 males as putative fathers, providing evidence that many of the animals identified on the Sakhalin feeding ground interbreed with each other, presumably while sharing a common migratory route. However, the success of the paternity assignment was lower than expected given the high proportion of sampled animals in this population, suggesting that some males which are contributing to reproduction may not use the primary western feeding ground on a regular basis. The combination of these results suggests that the population structure of gray whales in the North Pacific is more complex than previously thought, and that some movements between the eastern and western populations may take place. However, the maintenance of genetic differences between the two populations supports their recognition as separate eastern and western populations. Future efforts should focus on elucidating the nature and extent of any dispersal which is occurring in order to better understand factors potentially influencing the recovery of the small western populatio

Birth-Intervals and Sex Composition of Western Gray Whales Summering off Sakhalin Island, Russia

Determining the birth-interval at which reproductive females produce calves is an indispensable component of studies on the population biology of large whales. In theory, shorter birth-intervals will result in a faster rate of population increase. Therefore, estimating this reproductive parameter is particularly important for modeling exercises designed to project the potential growth of a given population and, in the case of endangered populations, their ability to recover from a depleted state (e.g. Cooke et al., 2008). While a number of inherent biases exist with respect to determination of birth-intervals for baleen whales (Barlow and Clapham, 1997), dedicated sampling efforts and long-term field studies of known individuals have provided significant insight regarding this variable for a number of large whale populations. Knowing the ratio of males to females, including the primary, secondary, and tertiary sex ratio in a population is also essential to demographic assessments. In general, sex ratio information for baleen whale populations is patchy and, as true for birth-interval data, subject to a broad range of sampling bias.br\u3e Despite the aforementioned limitations, valuable information on the birth-interval and sex ratio of eastern Pacific gray whales (Eschrichtius robustus) has been published (e.g. Rice and Wolman, 1971; Rice, 1983; Jones, 1990). These studies, drawing upon biological samples collected from stranded or hunted individuals and photo-identification data from free-ranging whales, indicate that the typical birth-interval for the eastern gray whale is two-years, with a gestation period of about 418 days and lactation period of 6-8 months (Rice and Wolman, 1971; Rice, 1983). The fetal sex ratio for eastern gray whales has been estimated to be 1:1 (Rice, 1983). The western Pacific gray whale population is critically endangered, numbering only about 130 individuals, and its ability to recover from near extinction is questionable (Cooke et al., 2008; Weller et al., 2008). Given the small size of the population and a relatively short period of study, fewer data exist regarding the birth-interval and sex ratio of western gray whales compared to the available information on eastern gray whales. This paper presents preliminary analysis of birth-intervals and sex composition of western gray whales summering off northeastern Sakhalin Island, Russia. Calving data were examined to determine the range of birth-interval values, the relative frequencies of different birth-intervals, and if calving intervals for individual females were stable or variable. In addition, determining the sex of calves and non-calves observed during the 12-year study allowed sex composition of the population to be assessed, including an examination of the proportion of male vs. female calves born to individual females

Comparing Observations of Age at First Reproduction in Western Gray Whales to Estimates of Age at Sexual Maturity in Eastern Gray Whales

Age at first reproduction (AFR) is a basic component of age-structured whale assessment models, but direct estimates of this parameter do not exist for either the abundant eastern or critically endangered western population of gray whales (Eschrichtius robustus). Instead, assessments of both populations have utilized either of two recognized estimates of eastern gray whale age at sexual maturity (ASM) that are adjusted by a year to account for fetal gestation. These ASM estimates are: 1) 9 years median, 6-12 years range, and 2) 6 years median, 5-9 years range, but there are biases and discrepancies associated with these estimates. Over a decade of individual monitoring of western gray whales on their primary feeding ground off the northeastern coast of Sakhalin Island, Russia, has identified 17 female whales first sighted as calves or yearlings that were potentially sexually mature by the 2009 field season, ranging in age from 5 to 11 years. However, only two of these whales have been observed to have produced a calf, establishing the first observed values of western gray whale AFR as seven and 11 years. While limiting, that only two AFR observations were made is also informative, suggesting that until more information is available, the first eastern gray whale ASM estimate is the more appropriate to use in western gray whale assessments. Overall, eastern and western gray whale assessments would benefit from a concerted effort to collect AFR observations from each population

MateBruceHMSCAssessmentGeneticStructure_TableS1-S3.pdf

Although most eastern North Pacific (ENP) gray whales feed in the Bering, Beaufort, and Chukchi Seas during summer and fall, a small number of individuals, referred to as the Pacific Coast Feeding Group (PCFG), show intra- and interseasonal fidelity to feeding areas from northern California through southeastern Alaska. We used both mitochondrial DNA (mtDNA) and 12 microsatellite markers to assess whether stock structure exists among feeding grounds used by ENP gray whales. Significant mtDNA differentiation was found when samples representing the PCFG (n = 71) were compared with samples (n = 103) collected from animals feeding further north (Fₛₜ = 0.012, P = 0.0045). No significant nuclear differences were detected. These results indicate that matrilineal fidelity plays a role in creating structure among feeding grounds but suggests that individuals from different feeding areas may interbreed. Haplotype diversities were similar between strata (hₚCFG = 0.945, hₙₒᵣₜₕₑᵣₙ = 0.952), which, in combination with the low level of mtDNA differentiation identified, suggested that some immigration into the PCFG could be occurring. These results are important in evaluating the management of ENP gray whales, especially in light of the Makah Tribe’s proposal to resume whaling in an area of the Washington coast utilized by both PCFG and migrating whales.Keywords: Gray whale, Eschrichtius robustus, Microsatellites, Population structure, Mitochondrial DNA, Demographic independenc

MateBruceHMSCAssessmentGeneticStructure.pdf

Although most eastern North Pacific (ENP) gray whales feed in the Bering, Beaufort, and Chukchi Seas during summer and fall, a small number of individuals, referred to as the Pacific Coast Feeding Group (PCFG), show intra- and interseasonal fidelity to feeding areas from northern California through southeastern Alaska. We used both mitochondrial DNA (mtDNA) and 12 microsatellite markers to assess whether stock structure exists among feeding grounds used by ENP gray whales. Significant mtDNA differentiation was found when samples representing the PCFG (n = 71) were compared with samples (n = 103) collected from animals feeding further north (Fₛₜ = 0.012, P = 0.0045). No significant nuclear differences were detected. These results indicate that matrilineal fidelity plays a role in creating structure among feeding grounds but suggests that individuals from different feeding areas may interbreed. Haplotype diversities were similar between strata (hₚCFG = 0.945, hₙₒᵣₜₕₑᵣₙ = 0.952), which, in combination with the low level of mtDNA differentiation identified, suggested that some immigration into the PCFG could be occurring. These results are important in evaluating the management of ENP gray whales, especially in light of the Makah Tribe’s proposal to resume whaling in an area of the Washington coast utilized by both PCFG and migrating whales.Keywords: Microsatellites, Demographic independence, Eschrichtius robustus, Population structure, Gray whale, Mitochondrial DN

Western Gray Whales off Sakhalin Island, Russia: A Joint Russia-U.S. Scientific Investigation July-September 2003

Research on the western gray whale (Eschrichtius robustus) population summering off northeastern Sakhalin Island, Russia, has been ongoing since 1995. This collaborative Russia-U.S. research program has produced important new information on the present day conservation status of this critically endangered population. This report reviews recent findings from 2003 research activities and combines such with data from previous years, in some cases ranging back to 1994. Photo-identification research conducted off Sakhalin Island in 2003 resulted in the identification of 75 whales, including 11 calves and two previously unidentified non-calves. When combined with data from 1994-2002, a catalog of 131 photo-identified individuals has been compiled. The population size is estimated to be approximately 100 individuals and non-calf and calf survival rates are 0.95 and 0.70, respectively. Of the 131 whales photo-identified, 108 (82.4%) have now been biopsy sampled. From genetic analysis of samples collected through 2002, an overall male biased sex ratio of 59.1% males and 40.9% females was determined. The sex ratio for calves was 68.0% male and 32.0% female. Previous genetic research on the western gray whale population documented clear genetic differentiation from the eastern population on the basis of mitochondrial DNA haplotype frequencies. Nuclear DNA markers used to measure the differentiation and relative levels of genetic diversity in the nuclear genome between the western and eastern populations confirm the earlier conclusion (based on mtDNA) that the two populations are genetically distinct and further suggests negligible gene flow of either sex between populations. A minimum of 23 reproductive females has been observed since 1995 and their most common (74.4%) calving interval is three or more years. Three whales were recorded as skinny” in 2003, a total number lower than recorded in previous years. In addition to the clear biological difficulties that western gray whales are facing, the recent onset of large-scale oil and gas development programs near their summer feeding ground pose new threats to the future survival of the population