Model fitting and hypothesis testing for age-specific mortality data

Demographic studies focusing on age-specific mortality rates are becoming increasingly common throughout the fields of life-history evolution, ecology and biogerontology. Well-defined statistical techniques for quantifying patterns of mortality within a cohort and identifying differences in age-specific mortality among cohorts are needed. Here I discuss using maximum likelihood (ML) statistical methods to estimate the parameters of mathematical models, which are used to describe the change in mortality with age. ML provides a convenient and powerful framework for choosing an adequate mortality model, estimating model parameters and testing hypotheses about differences in parameters among experimental or ecological treatments. Simulations suggest that experiments designed to estimate age-specific mortality should involve at least 100-500 individuals per cohort per treatment. Significant bias in the estimation of model parameters is introduced when the mortality model is misspecified and samples are too small to detect the true mortality pattern. Furthermore, the lack of simple and efficient procedures for comparing different mortality models has forced the use of the Gompertz model, which specifies an exponentially increasing mortality with age, and which may not apply to the majority of experimental systems.     

Before senescence: the evolutionary demography of ontogenesis

The age-specific mortality curve for many species, including humans, is U-shaped: mortality declines with age in the developing cohort (ontogenescence) before increasing with age (senescence). The field of evolutionary demography has long focused on understanding the evolution of senescence while largely failing to address the evolution of ontogenescence. The current review is the first to gather the few available hypotheses addressing the evolution of ontogenescence, examine the basis and assumptions of each and ask what the phylogenetic extent of ontogenescence may be. Ontogenescence is among the most widespread of life-history traits, occurring in every population for which I have found sufficiently detailed data, in major groups throughout the eukaryotes, across many causes of death and many life-history types. Hypotheses seeking to explain ontogenescence include those based on kin selection, the acquisition of robustness, heterogeneous frailties and life-history optimization. I propose a further hypothesis, arguing that mortality drops with age because most transitions that could trigger the risks caused by genetic and developmental malfunctions are concentrated in early life. Of these hypotheses, only those that frame ontogenescence as an evolutionary by-product rather than an adaptation can explain the tremendous diversity of organisms and environments in which it occurs.     

Age-specific mortality rates in reef fishes: Evidence and implications

Abstract Mortality is a fundamental demographic rate, the nature of which has profound consequences for both the dynamics of populations and the life-history evolution of species. For example, if per capita mortality rates are age- or stage-specific, life-history traits should evolve in response to age- and stage-specific differences in selection arising from these temporally variable rates. Similarly, variation in the average mortality rate across ages and/or stages can also select for shifts in life history. Mortality rates of recently settled reef fishes can be very high and per capita mortality is commonly assumed to decrease with increasing age. A review of evidence for age-specific per capita mortality rates in reef fishes from early postsettlement up to 13 months postsettlement suggests that during this period these rates are often age invariant. The data on which these interpretations are based, however, are extremely limited both in terms of the proportion of the life cycle over which mortality rates have been sampled and the quality of these data. Nonetheless, these data do suggest that selective pressures associated with patterns of mortality may vary among species of reef fishes and that these species therefore could be more effectively used in the study of life-history evolution. At present, reef fishes are under-represented in the study of life-history evolution compared with other vertebrate taxa.     

High adult mortality among Hiwi hunter-gatherers: implications for human evolution

Extant apes experience early sexual maturity and short life spans relative to modern humans. Both of these traits and others are linked by life-history theory to mortality rates experienced at different ages by our hominin ancestors. However, currently there is a great deal of debate concerning hominin mortality profiles at different periods of evolutionary history. Observed rates and causes of mortality in modern hunter-gatherers may provide information about Upper Paleolithic mortality that can be compared to indirect evidence from the fossil record, yet little is published about causes and rates of mortality in foraging societies around the world. To our knowledge, interview-based life tables for recent hunter-gatherers are published for only four societies (Ache, Agta, Hadza, and Ju/'hoansi). Here, we present mortality data for a fifth group, the Hiwi hunter-gatherers of Venezuela. The results show comparatively high death rates among the Hiwi and highlight differences in mortality rates among hunter-gatherer societies. The high levels of conspecific violence and adult mortality in the Hiwi may better represent Paleolithic human demographics than do the lower, disease-based death rates reported in the most frequently cited forager studies.     

Population studies: Animal ecology and demography

This concluding survey of the problems considered in the Symposium naturally falls into three sections. In the first brief section certain of the areas in which there is considerable difference in outlook are discussed with a view to ascertaining the nature of the differences in the points of view of workers in different parts of the field; no aspect of the Symposium has been more important than the reduction of areas of dispute. In the second section a rather detailed analysis of one particular problem is given, partly because the question, namely, the nature of the ecological niche and the validity of the principles of niche specificity has raised and continues to raise difficulties, and partly because discussion of this problem gives an opportunity to refer to new work of potential importance not otherwise considered in the Symposium. The third section deals with possible directions for future research. Concluding remarks reprinted from theCold Spring Harbor Symposia on quantitative Biology, Vol. 22, pp. 415–427 (1957) with the permission of the Long Island Biological Association.     

Oxidative stress in ecology and evolution: lessons from avian studies

Although oxidative stress is a central topic in biochemical and medical research, the number of reports on its relevance in life‐history studies of non‐human animals is still low. Information about oxidative stress in wild birds may help describe functional interactions among the components of life‐history traits. Currently available evidence suggests that oxidative stress may impart an important physiological cost on longevity, reproduction, immune response or intense physical activity. Given the gaps in our present knowledge, it is still premature to attempt to draw definitive conclusions and basic questions (e.g. how is oxidative stress generated and how do organisms cope with it?) have yet to be fully explored under natural conditions. Therefore, caution is needed in developing hypotheses or drawing general conclusions until additional data become available to perform more rigorous comparative analyses.     

Predation, group size and mortality in a cooperative mongoose, Suricata suricatta

1. In social mammals where group members cooperate to detect predators and raise young, members of small groups commonly show higher mortality or lower breeding success than members of large ones. It is generally assumed that this is because large group size allows individuals to detect or repel predators more effectively but other benefits of group size may also be involved, including reduced costs of raising young and more effective competition for resources with neighbouring groups.
2. To investigate the extent to which predation rate affects survival, we compared mortality rates in two populations of suricates ( Suricata suricatta ), one living in an area of high predator density (Kalahari Gemsbok Park) and one living in an area of relatively low predator density (neighbouring ranchland). Most aspects of feeding ecology and growth (including time spent feeding, daily weight gain, growth, adult body weight, breeding frequency and neonatal mortality) were similar in the two populations. In contrast, mortality of animals over 3 months old was 1·7 times higher in the Park than on ranchland.
3. Mortality of juveniles between emergence from the natal burrow and 6 months of age was higher in small groups than large ones in the Park but significantly lower in small groups than large ones on ranchland. Adult mortality declined in larger groups in both areas.
4. The tendency for survival to be low in small groups had far-reaching consequences for the risk of group extinction. During a year of low rainfall in the Park, all groups of less than nine animals became extinct and population density declined to around a third of its initial level. We argue that high group extinction rates are to be expected in species where survival declines in small groups and mortality rates are high.     

The evolution of SMC proteins: phylogenetic analysis and structural implications

The SMC proteins are found in nearly all living organisms examined, where they play crucial roles in mitotic chromosome dynamics, regulation of gene expression, and DNA repair. We have explored the phylogenetic relationships of SMC proteins from prokaryotes and eukaryotes, as well as their relationship to similar ABC ATPases, using maximum-likelihood analyses. We have also investigated the coevolution of different domains of eukaryotic SMC proteins and attempted to account for the evolutionary patterns we have observed in terms of available structural data. Based on our analyses, we propose that each of the six eukaryotic SMC subfamilies originated through a series of ancient gene duplication events, with the condensins evolving more rapidly than the cohesins. In addition, we show that the SMC5 and SMC6 subfamily members have evolved comparatively rapidly and suggest that these proteins may perform redundant functions in higher eukaryotes. Finally, we propose a possible structure for the SMC5/SMC6 heterodimer based on patterns of coevolution.     

A coalescent framework for comparing alternative models of population structure with genetic data: evolution of Celebes toads

Isolation of populations eventually leads to divergence by genetic drift, but if connectivity varies over time, its impact on diversification may be difficult to discern. Even when the habitat patches of multiple species overlap, differences in their demographic parameters, molecular evolution and stochastic events contribute to differences in the magnitude and distribution of their genetic variation. The Indonesian island of Sulawesi, for example, harbours a suite of endemic species whose intraspecific differentiation or interspecific divergence may have been catalysed by habitat fragmentation. To further test this hypothesis, we have performed phylogenetic and coalescent-based analyses on molecular variation in mitochondrial and nuclear DNA of the Celebes toad (Bufo celebensis). Results support a role for habitat fragmentation that led to a population structure in these toads that closely matches distributions of Sulawesi macaque monkeys. Habitat fragmentation, therefore, may also have affected other groups on this island.     

Interaction of maternal protein and carbon monoxide on pup mortality in mice: implications for global infant mortality

BACKGROUND: The United States Surgeon General declared 2005 as the "Year of Healthy Child." To improve the health of all children, we need to start before pregnancy, with their mothers. Unfortunately, protein deficiency in the diets of poor pregnant mothers in developing countries is widespread. Carbon monoxide (CO) pollution is serious public health problem in developed and developing countries. METHODS: A two-way factorial experimental design was used. Mice were maintained on 27%, 16%, 8%, or 4% protein diets. Dams were exposed to 0 ppm (control), 65 ppm, or 125 ppm CO in air, in environmental chambers for 6 hr/day during the first 2 weeks of pregnancy. Controls were also subjected to environmental chamber conditions. Food and water were available at all times. Animals were allowed to deliver, and data on pup mortality was recorded. RESULTS: Litter size was not affected by CO exposure, but was directly related to the dietary protein levels. Pup weight was inversely related to the CO exposure level, and directly related to the dietary protein levels. Pup mortality on date of birth was increased by CO exposure and was inversely related to the dietary protein levels. Pup mortality at 1 week of age was increased by CO exposure and 55% of all pups died in 125 ppm CO exposed group. Pup mortality at 1 week of age was inversely related to dietary protein levels. All pups in the 4% dietary protein and in all concentrations of CO died. All pups in the 8% protein group and in all CO concentrations died except in 125 ppm CO group. Pup mortality in the 16% dietary protein group ranged from 14.8% in 0 ppm to 36.8% in 65 ppm CO groups. Pup mortality in the 27% dietary protein group ranged from 14.3% in the 0 ppm to 41.1% in the 125 ppm CO groups. CONCLUSIONS: DATA suggest that protein deficiency and CO exposure enhance pup mortality. The protein and CO also interact to increase pup mortality in 16% and 27% protein groups. Carbon monoxide exposure, along with protein deficiency during gestation, may be contributing factors for high rates of infant mortality in developing countries. The results of the study also suggest that un-vented combustion for heating and cooking, ambient pollution, and biomass smoke may have a major impact on the health of children worldwide; and may explain the causes of high infant mortality in poor countries and some sections of the United States population.     

Conservation implications for dingoes from the maternal and paternal genome: Multiple populations,dog introgression,and demography

It is increasingly common for apex predators to face a multitude of complex conservation issues. In Australia, dingoes are the mainland apex predator and play an important role in ecological functioning. Currently, however, they are threatened by hybridization with modern domestic dogs in the wild. As a consequence, we explore how increasing our understanding of the evolutionary history of dingoes can inform management and conservation decisions. Previous research on whole mitochondrial genome and nuclear data from five geographical populations showed evidence of two distinct lineages of dingo. Here, we present data from a broader survey of dingoes around Australia using both mitochondrial and Y chromosome markers and investigate the timing of demographic expansions. Biogeographic data corroborate the presence of at least two geographically subdivided genetic populations, southeastern and northwestern. Demographic modeling suggests that dingoes have undergone population expansion in the last 5,000 years. It is not clear whether this stems from expansion into vacant niches after the extinction of thylacines on the mainland or indicates the arrival date of dingoes. Male dispersal is much more common than female, evidenced by more diffuse Y haplogroup distributions. There is also evidence of likely historical male biased introgression from domestic dogs into dingoes, predominately within southeastern Australia. These findings have critical practical implications for the management and conservation of dingoes in Australia; particularly a focus must be placed upon the threatened southeastern dingo population.     

Death,demography and the denominator: Age-adjusted Influenza-18 mortality in Ireland

Using the Irish experience of the 1918–1919 Spanish flu pandemic (“Influenza-18”), we demonstrate how pandemic mortality statistics can be sensitive to the demographic composition of a country. We build a new spatially disaggregated population database for Ireland’s 32 counties for 1911–1920 with vital statistics on births, ageing, migration and deaths. Our principal contribution is to show why, and how, age-at-death data should be used to construct the age-standardised statistics necessary to make meaningful comparisons of mortality rates across time and space. We conclude that studies of the economic consequences of pandemics must better control for demographic factors if they are to yield useful policy-relevant insights. For example, while Northern Ireland had a higher crude death rate during the first wave of the Covid-19 pandemic, it also has an older population; age-adjusted mortality paints a very different picture.     

Retired flies,hidden plateaus,and the evolution of senescence in Drosophila melanogaster

Late‐life plateaus in age‐specific mortality have been an evolutionary and biodemographic puzzle for decades. Although classic theory on the evolution of senescence predicts late‐life walls of death, observations in experimental organisms document the opposite trend: a slowing in the rate of increase of mortality at advanced ages. Here, I analyze published life‐history data on individual Drosophila melanogaster females and argue for a fundamental change in our understanding of mortality in this important model system. Mortality plateaus are not, as widely assumed, exclusive to late life, and are not explained by population heterogeneity—they are intimately connected to individual fecundity. Female flies begin adult life in the working stage, a period of active oviposition and low but accelerating mortality. Later they transition to the retired stage, a terminal period characterized by limited fecundity and relatively constant mortality. Because ages of transition differ between flies, age‐synchronized cohorts contain a mix of working and retired flies. Early‐ and mid‐life plateaus are obscured by the presence of working flies, but can be detected when cohorts are stratified by retirement status. Stage‐specificity may be an important component of Drosophila life‐history evolution.     

Primate home range and GRIN2A, a receptor gene involved in neuronal plasticity: implications for the evolution of spatial memory

N -methyl- d -aspartate (NMDA) glutamate receptors play crucial roles in neuronal synaptic plasticity, learning and memory. However, as to whether different NMDA subunits are implicated in specific forms of memory is unclear. Moreover, nothing is known about the interspecific genetic variability of the GRIN2A subunit and how this variation can potentially explain evolutionary changes in behavioral phenotypes. Here, we used 28 primate GRIN2A sequences and various proxies of memory across primates to investigate the role of GRIN2A . Codon-specific sequence analysis on these sequences showed that GRIN2A in primates coevolved with a likely ecological proxy of spatial memory (relative home-range size) but not with other indices of non-spatial learning and memory such as social memory and social learning. Models based on gene averages failed to detect positive selection in primate branches with major changes in relative home-range size. This implies that accelerated evolution is concentrated in specific parts of the protein expressed by GRIN2A . Overall, our molecular evolution study, the first on GRIN2A , supports the notion that different NMDA subunits may play a role in specific forms of memory and that phenotypic diversity along with genetic evolution can be used to investigate the link between genes and behavior across evolutionary time.     

ABC as a flexible framework to estimate demography over space and time: some cons,many pros

The analysis of genetic variation to estimate demographic and historical parameters and to quantitatively compare alternative scenarios recently gained a powerful and flexible approach: the Approximate Bayesian Computation (ABC). The likelihood functions does not need to be theoretically specified, but posterior distributions can be approximated by simulation even assuming very complex population models including both natural and human‐induced processes. Prior information can be easily incorporated and the quality of the results can be analysed with rather limited additional effort. ABC is not a statistical analysis per se, but rather a statistical framework and any specific application is a sort of hybrid between a simulation and a data‐analysis study. Complete software packages performing the necessary steps under a set of models and for specific genetic markers are already available, but the flexibility of the method is better exploited combining different programs. Many questions relevant in ecology can be addressed using ABC, but adequate amount of time should be dedicated to decide among alternative options and to evaluate the results. In this paper we will describe and critically comment on the different steps of an ABC analysis, analyse some of the published applications of ABC and provide user guidelines.