Multistage time-to-event models improve survival inference by partitioning mortality processes of tracked organisms

Advances in tagging technologies are expanding opportunities to estimate survival of fish and wildlife populations. Yet, capture and handling effects could impact survival outcomes and bias inference about natural mortality processes. We developed a multistage time-to-event model that can partition the survival process into sequential phases that reflect the tagged animal experience, including handling and release mortality, post-release recovery mortality, and subsequently, natural mortality. We demonstrate performance of multistage survival models through simulation testing and through fish and bird telemetry case studies. Models are implemented in a Bayesian framework and can accommodate left, right, and interval censorship events. Our results indicate that accurate survival estimates can be achieved with reasonable sample sizes ( n ≈ 100 + ) and that multimodel inference can inform hypotheses about the configuration and length of survival stages needed to adequately describe mortality processes for tracked specimens. While we focus on survival estimation for tagged fish and wildlife populations, multistage time-to-event models could be used to understand other phenomena of interest such as migration, reproduction, or disease events across a range of taxa including plants and insects.

Testing frameworks for early life effects: the developmental constraints and adaptive response hypotheses do not explain key fertility outcomes in wild female baboons

In evolutionary ecology, two classes of explanations are frequently invoked to explain "early life effects" on adult outcomes. Developmental constraints (DC) explanations contend that costs of early adversity arise from limitations adversity places on optimal development. Adaptive response (AR) hypotheses propose that later life outcomes will be worse when early and adult environments are poorly "matched." Here, we use recently proposed mathematical definitions for these hypotheses and a quadratic-regression based approach to test the long-term consequences of variation in developmental environments on fertility in wild baboons. We evaluate whether low rainfall and/or dominance rank during development predict three female fertility measures in adulthood, and whether any observed relationships are consistent with DC and/or AR. Neither rainfall during development nor the difference between rainfall in development and adulthood predicted any fertility measures. Females who were low-ranking during development had an elevated risk of losing infants later in life, and greater change in rank between development and adulthood predicted greater risk of infant loss. However, both effects were statistically marginal and consistent with alternative explanations, including adult environmental quality effects. Consequently, our data do not provide compelling support for either of these common explanations for the evolution of early life effects.

Early life adversities and lifelong health outcomes: A review of the literature on large, social, long-lived nonhuman mammals

Social nonhuman animals are powerful models for studying underlying factors related to lifelong health outcomes following early life adversities (ELAs). ELAs can be linked to lifelong health outcomes depending on the species, system, sensitive developmental periods, and biological pathways. This review focuses on the literature surrounding ELAs and lifelong health outcomes in large, social, relatively long-lived nonhuman mammals including nonhuman primates, canids, hyenas, elephants, ungulates, and cetaceans. These mammals, like humans but unlike the most-studied rodent models, have longer life histories, complex social structures, larger brains, and comparable stress and reproductive physiology. Collectively, these features make them compelling models for comparative aging research. We review studies of caregiver, social, and ecological ELAs, often in tandem, in these mammals. We consider experimental and observational studies and what each has contributed to our knowledge of health across the lifespan. We demonstrate the continued and expanded need for comparative research to inform about the social determinants of health and aging in both humans and nonhuman animals.

Social and early life determinants of survival from cradle to grave: A case study in wild baboons

Field studies of natural mammal populations present powerful opportunities to investigate the determinants of health and aging using fine-grained observations of known individuals across the life course. Here, we synthesize five decades of findings from one such study: the wild baboons of the Amboseli ecosystem in Kenya. First, we discuss the profound associations between early life adversity, adult social conditions, and key aging outcomes in this population, especially survival. Second, we review potential mediators of the relationship between early life adversity and survival in our population. Notably, our tests of two leading candidate mediators-social isolation and glucocorticoid levels-fail to identify a single, strong mediator of early life effects on adult survival. Instead, early adversity, social isolation, and glucocorticoids are independently linked to adult lifespans, suggesting considerable scope for mitigating the negative consequences of early life adversity. Third, we review our work on the evolutionary rationale for early life effects on mortality, which currently argues against clear predictive adaptive responses. Finally, we end by highlighting major themes emerging from the study of sociality, development, and aging in the Amboseli baboons, as well as important open questions for future work.

Cumulative early-life adversity does not predict reduced adult longevity in wild gorillas

Extensive research across fields has repeatedly confirmed that early-life adversity (ELA) is a major selective force for many taxa, in part via its ties to adult health and longevity.1,2,3 Negative effects of ELA on adult outcomes have been documented in a wide range of species, from fish to birds to humans.4 We used 55 years of long-term data collected on 253 wild mountain gorillas to examine the effects of six putative sources of ELA on survival, both individually and cumulatively. Although cumulative ELA was associated with high mortality in early life, we found no evidence that it had detrimental consequences for survival later in life. Experiencing three or more forms of ELA was associated with greater longevity, with a 70% reduction in the risk of death across adulthood, driven specifically by greater longevity in males. Although this higher survival in later life is likely a consequence of sex-specific viability selection5 during early life due to the immediate mortality consequences of adverse experiences, patterns in our data also suggest that gorillas have significant resilience to ELA. Our findings demonstrate that the detrimental consequences of ELA on later life survival are not universal, and indeed largely absent in one of humans' closest living relatives. This raises important questions about the biological roots of sensitivity to early experiences and the protective mechanisms that contribute to resiliency in gorillas, which could be critical for understanding how best to encourage similar resiliency to early-life shocks in humans.

Testosterone histories from tusks reveal woolly mammoth musth episodes

Hormones in biological media reveal endocrine activity related to development, reproduction, disease and stress on different timescales¹. Serum provides immediate circulating concentrations², whereas various tissues record steroid hormones accumulated over time^3,4. Hormones have been studied in keratin, bones and teeth in modern^5-8 and ancient contexts^9-12; however, the biological significance of such records is subject to ongoing debate^10,13-16, and the utility of tooth-associated hormones has not previously been demonstrated. Here we use liquid chromatography with tandem mass spectrometry paired with fine-scale serial sampling to measure steroid hormone concentrations in modern and fossil tusk dentin. An adult male African elephant (Loxodonta africana) tusk shows periodic increases in testosterone that reveal episodes of musth^17-19, an annually recurring period of behavioural and physiological changes that enhance mating success^20-23. Parallel assessments of a male woolly mammoth (Mammuthus primigenius) tusk show that mammoths also experienced musth. These results set the stage for wide-ranging studies using steroids preserved in dentin to investigate development, reproduction and stress in modern and extinct mammals. Because dentin grows by apposition, resists degradation, and often contains growth lines, teeth have advantages over other tissues that are used as records of endocrine data. Given the low mass of dentin powder required for analytical precision, we anticipate dentin-hormone studies to extend to smaller animals. Thus, in addition to broad applications in zoology and palaeontology, tooth hormone records could support medical, forensic, veterinary and archaeological studies.

Identifying the Effects of Social Disruption through Translocation on African Elephants (Loxodonta africana), with Specifics on the Social and Ecological Impacts of Orphaning

African elephants (Loxodonta africana) exhibit a long developmental period during which they acquire complex social and ecological knowledge through social networks. Central to this is that matriarchs and older individuals play an important role as repositories of information gained through experience. Anthropogenic interventions-including poaching, culling, translocation, and hunting-can disrupt elephants' social networks, with implications for individual fitness and potential long-term population viability. Here, we draw on a unique long-running, individual-based dataset to examine the impacts of translocation on a population of elephants in South Africa, taking into consideration demographic rates, social dynamics, and ecological decision-making. Specifically, we compared two translocated groups: a group of unrelated culling Orphans and a family herd. We found that the Orphan group experienced accelerated reproductive rates when compared with the family herd. The Orphan group also fissioned more frequently and for longer periods of time, suggesting lower cohesiveness, and were less decisive in their large-scale movement decisions. These results add to the growing body of literature on the downstream impacts of social disruption for elephants. Whilst the translocation of culling Orphans is no longer practised in South Africa, we encourage careful consideration of any elephant translocation and the resulting social disruption.

Gastric cancer incidence trends in China and Japan from 1990 to 2019: Disentangling age-period-cohort patterns

BACKGROUND

Recent data have shown divergent trends in gastric cancer (GC) incidence between China and Japan; however, the cause for has not been explored.

METHODS

We retrieved GC incidence data from 1990 to 2019 from the Global Burden of Disease study, stratified by sex for both countries. We analyzed annual average percentage change (AAPC) via a joinpoint regression model and estimated the effects of age, period, and cohort via the age-period-cohort model.

RESULTS

The age-standardized incidence rate trends for GC decreased in both countries and both sexes, but the reduction was more pronounced in Japan because the AAPC for Japanese males (AAPC = -2.65%; 95% CI, -2.98 to -2.32) was eight times greater than that of Chinese males (AAPC = -0.30%; 95% CI, -0.5 to -0.09). The age and cohort effects on the trend are similar in both countries: the risk of GC incidence increased with age among the Chinese and the Japanese but was lower among younger birth cohorts. The two countries showed contrasting trends over the study period; although the risk of GC rapidly decreased for Japanese males and females, it increased by twofold among Chinese males.

CONCLUSIONS

The period effect is the main reason for the divergent trends in age-standardized incidence rate for GC in China and Japan. By comparing national cancer control programs in both countries, we concluded that countries with a high prevalence of GC, such as China, can learn from Japan's experience in controlling GC by actively conducting national population screening, which is expected to facilitate both prevention and treatment of GC.

LAY SUMMARY

More than one-half of all new gastric cancer (GC) worldwide occur in China and Japan, but the reasons for the different incidence trends have not been thoroughly analyzed. Analysis using the age-period-cohort model confirmed that the cohort effect was the main reason for the decline in age-standardized incidence rate (ASIR) for GC and that the period effect may be the main reason for the divergent trends in gastric cancer ASIR in China and Japan.

Long-term trends in elephant mortality and their causes in Kenya

High mortality poses a serious threat to sustainable conservation of the African elephant (Loxodonta africana). Using detected carcass data collected by the Kenya Wildlife Service (KWS) during 1992-2017, we analyze temporal and spatial variation in elephant mortality in Kenya. We investigate the major mortality causes and means used to kill elephants, carcass category, tusk recovery status, variation in mortality with elephant age and sex classes, differences between inside and outside protected areas (PAs), the Proportion of Illegally Killed Elephants (PIKE) and the overall mortality rate (MR — the number of dead/number of live elephants in a given year). In total 9,182 elephant deaths were recorded during the 26 years. Elephant mortality increased over time and was attributed primarily to natural (33.1%) and human-related causes, particularly ivory poaching (31.5%) and human-elephant conflicts (19.9%). Elephant mortality varied across Kenya’s 47 counties in correspondence with variation in elephant population size and was the highest in the leading elephant range counties of Taita Taveta, Laikipia, Samburu and Meru. Mortality was higher for males and adults and outside the protected areas. Most elephant carcasses had tusks (75.1%) but a few did not (12.5%). Yearly PIKE values peaked in 2012, the year with the highest poaching levels in Kenya during 1992-2017. MR increased throughout 1992-2017. Temporal variation in elephant mortality probability was significantly influenced by human and livestock population densities, average annual maximum temperature and total annual rainfall and the strength of these influences varied across the seven leading elephant range counties of Kenya. Natural processes are increasingly contributing to elephant mortality likely due to climate change and the associated food and water stress, exacerbated by contracting range. Enhancing anti-poaching and strategies for mitigating climate change impacts and human-elephant conflict and reducing range contraction while sustaining habitat connectivity can help reduce mortality and promote elephant conservation. Strengthening enforcement of international wildlife laws can further reduce illegal trade in tusks and killing of elephants.

Cohort consequences of drought and family disruption for male and female African elephants

Cohort effects, reflecting early adversity or advantage, have persisting consequences for growth, reproductive onset, longevity, and lifetime reproductive success. In species with prolonged life histories, cohort effects may establish variation in age-sex structures, while social structure may buffer individuals against early adversity. Using periods of significant ecological adversity, we examined cohort effects for male and female elephants (Loxodonta africana) over almost 50 years in Amboseli, Kenya. Mortality spiked during severe droughts with highest mortality among calves under 2 years and females over 40 years. Deaths of oldest females resulted in social disruption via matriarch turnover, with potential impacts on resource acquisition for survivors. We predicted that survivors of high mortality and social challenges would have altered life-history trajectories, with later age at first reproduction and reduced age-specific fertility for females and slow transitions to independence and late-onset of potential mating or musth among males. Contrary to expectations, there were no persisting early drought effects on female age at first conception while matriarch loss around puberty accelerated reproductive onset. Experience of an early life drought did not influence age-specific reproductive rates once females commenced reproduction. Males who survived an early drought exhibited complex consequences: male age at family independence was later with larger peer cohort size, but earlier with drought in year of independence (13.9 vs 14.6 years). Early drought had no effect on age at first musth, but male reproductive onset was weakly associated with the number of peers (negative) and age at independence (positive).