BaSTA: an R package for Bayesian estimation of age‐specific survival from incomplete mark–recapture/recovery data with covariates

Colchero, Fernando; Jones, Owen R.; Rebke, Maren

doi:10.1111/j.2041-210x.2012.00186.x

Cited by 131 publications

(163 citation statements)

References 26 publications

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“…These individuals included the 600 used in the analyses above but also included turtles with unknown ages that were captured from 1993 to 2012. To test for a signature of demographic senescence in mortality, accelerating mortality models were fit to mark-recapture data for both known age and unknown age females using a Bayesian hierarchical analysis (48,49). DIC was used to choose among alternative models for the survival function fit using the BaSTA (Bayesian Survival Trajectory Analysis) package (48) (version 1.3) in R (version 2.14; R development Core Team 2011) ( Table 2).…”

Section: Methodsmentioning

confidence: 99%

Decades of field data reveal that turtles senesce in the wild

Warner

Miller

Bronikowski

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Lifespan and aging rates vary considerably across taxa; thus, understanding the factors that lead to this variation is a primary goal in biology and has ramifications for understanding constraints and flexibility in human aging. Theory predicts that senescence-declining reproduction and increasing mortality with advancing age-evolves when selection against harmful mutations is weaker at old ages relative to young ages or when selection favors pleiotropic alleles with beneficial effects early in life despite late-life costs. However, in many long-lived ectotherms, selection is expected to remain strong at old ages because reproductive output typically increases with age, which may lead to the evolution of slow or even negligible senescence. We show that, contrary to current thinking, both reproduction and survival decline with adult age in the painted turtle, Chrysemys picta, based on data spanning >20 y from a wild population. Older females, despite relatively high reproductive output, produced eggs with reduced hatching success. Additionally, age-specific mark-recapture analyses revealed increasing mortality with advancing adult age. These findings of reproductive and mortality senescence challenge the contention that chelonians do not age and more generally provide evidence of reduced fitness at old ages in nonmammalian species that exhibit long chronological lifespans.aging | lifespan | painted turtle | reproduction | senescence W hy do some organisms show little to no signs of aging as they get older, whereas others exhibit substantial physiological deterioration and reproductive senescence with advancing age (1, 2)? This question has motivated many studies of aging in the wild, ranging from reviews of demographic aging (3, 4) to compilations of mechanistic studies (e.g., ref. 5 and references therein). Senescence should evolve when selection is weaker on deleterious traits expressed at an old age relative to those expressed at a young age (6). Indeed, mutations with senescent effects can persist because of a tradeoff between beneficial effects early in life and pleiotropic detrimental effects late in life (7,8). Importantly, the persistence of age-specific deleterious mutations will therefore be influenced by levels and sources of extrinsic mortality (e.g., predation, resource scarcity, infectious disease) and the particular ages at which extrinsic sources cause death (9, 10). For example, the onset of physiological or reproductive deterioration is expected to occur relatively early in populations exposed to high levels of extrinsic mortality of adults. Accordingly, such organisms are expected to evolve rapid development/growth, high reproductive effort at young ages, and a shortened lifespan. For species or populations that experience low extrinsic mortality rates, physiological and reproductive function are expected to decline more slowly with advancing age or with a delay in the onset of senescent decline (7). Moreover, such age-specific selection dynamics can result in negligible (11) and even negative ...

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Section: Methodsmentioning

confidence: 99%

Decades of field data reveal that turtles senesce in the wild

Warner

Miller

Bronikowski

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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“…In our analyses we used the R package BaSTA [Colchero et al, 2012; Colchero & Clark, 2012], an algorithm for age-specific survival analysis when age information is missing. This method has been showed to recover unbiased estimates of mortality with small sample sizes.…”

Section: Introductionmentioning

confidence: 99%

Age and sex‐specific mortality of wild and captive populations of a monogamous pair‐bonded primate (Aotus azarae)

Larson¹,

Colchero

Jones

et al. 2015

American J Primatol

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In polygynous primates, a greater reproductive variance in males have been linked to their reduced life expectancy relative to females. The mortality patterns of monogamous pair-bonded primates, however, are less clear. We analyzed the sex differences in mortality within wild (NMales = 70, NFemales = 73) and captive (NMales = 25, NFemales = 29) populations of Azara’s owl monkeys (Aotus azarae), a socially and genetically monogamous primate exhibiting biparental care. We used Bayesian Survival Trajectory Analysis (BaSTA) to test age-dependent models of mortality. The wild and captive populations were best fit by the logistic and Gompertz models, respectively, implying greater heterogeneity in the wild environment likely due to harsher conditions. We found that age patterns of mortality were similar between the sexes in both populations. We calculated life expectancy and disparity, the latter a measure of the steepness of senescence, for both sexes in each population. Males and females had similar life expectancies in both populations; the wild population overall having a shorter life expectancy than the captive one. Furthermore, captive females had a reduced life disparity relative to captive males and to both sexes in the wild. We interpret this pattern in light of the hazards associated with reproduction. In captivity, where reproduction is intensely managed, the risks associated with gestation and birth are tempered so that there is a reduction in the likelihood of captive females dying prematurely, decreasing their overall life disparity.

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“…We used an extension of the Bayesian approach proposed by Barthold et al (13) to model age-and sex-specific mortality for species where one or both sexes undergo natal dispersal. The model builds upon the Bayesian survival trajectory analysis framework (63,64) to model sex-specific mortality. We extended the model to include species for which one or both sexes undergo higher-order 13 and 14).…”

Section: Smoothing Of Life-mentioning

confidence: 99%

The emergence of longevous populations

Colchero

Rau

Jones

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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159

165

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The human lifespan has traversed a long evolutionary and historical path, from short-lived primate ancestors to contemporary Japan, Sweden, and other longevity frontrunners. Analyzing this trajectory is crucial for understanding biological and sociocultural processes that determine the span of life. Here we reveal a fundamental regularity. Two straight lines describe the joint rise of life expectancy and lifespan equality: one for primates and the second one over the full range of human experience from average lifespans as low as 2 y during mortality crises to more than 87 y for Japanese women today. Across the primate order and across human populations, the lives of females tend to be longer and less variable than the lives of males, suggesting deep evolutionary roots to the male disadvantage. Our findings cast fresh light on primate evolution and human history, opening directions for research on inequality, sociality, and aging.biodemography | equality | lifespan | pace and shape | senescence L ongevous populations have two characteristics: The average length of life is long and relative variation in lifespans is low. For example, life tables for contemporary Sweden and Japan indicate that most deaths occur at ages between the late 70s and early 90s. Our primate relatives, in contrast, have lifespans that are highly variable in length but short on average and rarely longer than 30 y (Fig. 1). An association between the average length of life and its variability has been found for industrialized societies (1, 2). However, detailed knowledge is lacking about whether and how this association varies across species separated by millions of years of primate evolution or whether it has changed over the past several centuries of unprecedented social progress in human populations. Fuller comprehension of the relationship between rising lifespans and reduced lifespan variability across evolution and history holds potential insights that might illuminate past, current, and future longevity.We pose three related questions aimed at filling this knowledge gap: How long and variable are lifespans for humans compared with nonhuman primates, for humans today compared with the past, and for males compared with females? We provide answers to these questions by applying a powerful framework that simultaneously examines changes in both the average length of life in a population or species-the "pace" of life-and relative variation in the length of life, i.e., the "shape" of the distribution of ages at death (3-5). Studying variation in lifespan links to increasing interest in social, economic, and health inequalities and to key sociological findings that relate social factors-including high social status and social integration-to longer, healthier lifespans in human and animal societies (6-10).Estimating the average length of life (here measured by life expectancy, the mean age at death) and variation in lifespans relative to the average (measured here as "lifespan equality"; Box 1) requires data on the ages at death of individuals...

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BaSTA: an R package for Bayesian estimation of age‐specific survival from incomplete mark–recapture/recovery data with covariates

Cited by 131 publications

References 26 publications

Decades of field data reveal that turtles senesce in the wild

Decades of field data reveal that turtles senesce in the wild

Age and sex‐specific mortality of wild and captive populations of a monogamous pair‐bonded primate (Aotus azarae)

The emergence of longevous populations

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