Estimating the effect of inbreeding on survival

Conservation biologists need to be able to estimate reliably the effects of inbreeding on survival, and need to be able to do so with a range of different data types. Kalinowski and Hedrick described a non-linear maximum likelihood estimation procedure for modelling relationships between survivorship and inbreeding. Although their method is useful for illustrating the concepts involved in modelling such relationships, it is only applicable to simple datasets. We illustrate that the parameter estimates generated by Kalinowski and Hedrick's method are easily obtained using generalized linear modelling procedures available in standard statistical packages, and that these offer several advantages even with simple datasets. We suggest procedures that can be used for modelling relationships between survival and inbreeding with more complex data types, including datasets with multiple and ragged encounters, uncertain detection and random effects.     

Testing the ratio of two poisson rates

In this paper we compare the properties of four different general approaches for testing the ratio of two Poisson rates. Asymptotically normal tests, tests based on approximate p -values, exact conditional tests, and a likelihood ratio test are considered. The properties and power performance of these tests are studied by a Monte Carlo simulation experiment. Sample size calculation formulae are given for each of the test procedures and their validities are studied. Some recommendations favoring the likelihood ratio and certain asymptotic tests are based on these simulation results. Finally, all of the test procedures are illustrated with two real life medical examples.     

Estimating rate constants from single ion channel currents when the initial distribution is known

Single ion channel currents can be analysed by hidden or aggregated Markov models. A classical result from Fredkin et al. (Proceedings of the Berkeley conference in honor of Jerzy Neyman and Jack Kiefer, vol I, pp 269–289, 1985) states that the maximum number of identifiable parameters is bounded by 2n_on_c, where n_o and n_c denote the number of open and closed states, respectively. We show that this bound can be overcome when the probabilities of the initial distribution are known and the data consist of several sweeps.     

Inconsistency of the maximum parsimony method when the rate of nucleotide substitution is constant

The inconsistency of the maximum parsimony method is known to occur even when the rate of nucleotide substitution is constant. To understand why this inconsistency occurs, a mathematical study was conducted for the cases of five, six, and seven sequences. The results obtained indicate that this inconsistency occurs because the probability of occurrence of nucleotide configurations generated by one substitution on a short interior branch is often lower than that of configurations generated by more substitutions on other longer branches. The chance of occurrence of this event—or, the inconsistency of the maximum parsimony method—apparently increases as the number of sequences increases. The inconsistency may occur even when the extent of sequence divergence is relatively small. Correspondence to: M. Nei     

Recovery rates of bottlenose dolphin (Tursiops truncatus) carcasses estimated from stranding and survival rate data

Recovery of cetacean carcasses provides data on levels of human‐caused mortality, but represents only a minimum count of impacts. Counts of stranded carcasses are negatively biased by factors that include at‐sea scavenging, sinking, drift away from land, stranding in locations where detection is unlikely, and natural removal from beaches due to wave and tidal action prior to detection. We estimate the fraction of carcasses recovered for a population of coastal bottlenose dolphins (Tursiops truncatus), using abundance and survival rate data to estimate annual deaths in the population. Observed stranding numbers are compared to expected deaths to estimate the fraction of carcasses recovered. For the California coastal population of bottlenose dolphins, we estimate the fraction of carcasses recovered to be 0.25 (95% CI = 0.20–0.33). During a 12 yr period, 327 animals (95% CI = 253–413) were expected to have died and been available for recovery, but only 83 carcasses attributed to this population were documented. Given the coastal habits of California coastal bottlenose dolphins, it is likely that carcass recovery rates of this population greatly exceed recovery rates of more pelagic dolphin species in the region.     

The influence of constant and fluctuating temperatures on development rate and survival of pupae of the Australian sheep blowfly Lucilia cuprina

Functions describing instantaneous development rates in constant and natural temperature regimes were obtained for pupae of the Australian sheep blowfly, Lucilia cuprina (Wiedemann). These were derived using a technique that directly calculates rate functions from development-time observations made under any temperature regime. The functions indicated similar instantaneous development rates for constant and natural temperatures up to 30°C. At 30° the constant-temperature function reached a plateau which was maintained to the constant-temperature thermal limit. The natural-temperature function, however, continued its ascending phase to 34°, and then fell sharply to zero at 42°.The median survival temperatures of pupae for single 7-h exposures, daily 7-h exposures, and continuous exposures to high temperatures were 44.7, 39.2, and 34.4°, respectively. Development was completed at constant 15° but not at 10°. Median survival times at constant 10, 5, 0 and-5° were 4.3, 4.2, 2.5 and 1.5 days. Mortality was slight for single or daily 7-h exposures to-5°, but was complete for all except brief single exposures to-10°.

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Influence des températures constantes et de la thermopériode sur le taux de développement et la survie des pupes de Lucilia cuprina

Résumé Des fonctions associant les taux de développement aux températures en conditions constantes et en thermopériodes naturelles ont été établies pour les pupes de L. cuprina. La fonction pour les conditions naturelles décrit les taux de développement immédiat-c'est-à-dire les taux de développement existant en réponse à la température pour chaque laps de temps (en réalité, pour un court intervalle), plutôt que le taux moyen pour une gamme de températures. La fonction pour les températures constantes décrit à la fois les taux de développement instantané et moyen (ceux-ci étant équivalents, en ne supposant pas de réponses spécifiques suivant l'âge en conditions constantes). Les fonctions ont été dérivées en utilisant une technique qui calcule directement les fonctions des taux à partir des observations sur les durées de développement faites dans chaque condition de température.Les fonctions ont révélé des taux de développement instantanés semblables pour les températures jusqu'à 30°C. A 30°C la fonction pour la température constante a atteint un plateau qui s'est maintenu jusqu'à la limite thermique. La fonction pour les thermopériodes naturelles a continué de s'élever jusqu'a 34°C, et alors a chuté brutalement jusqu'à zéro à 42°C. Dans la région d'où les lots de pupes ont été obtenus les températures subies par les pupes dans les zones non ombragées dépassent fréquemment 50°C pendant l'été. Les taux de développement des pupes aux températures au dessus de 30°C, où les fonctions avec températures constantes et thermopériodes deviennent différentes, sont cependant cohérent avec les expériences dans la nature avec L. cuprina. Les températures médianes de survie des pupes pour une exposition unique de 7 h, pour des expositions quotidiennes de 7 h et pour une exposition constante à haute température étaient respectivement de 44,7; 39, 2 et 34,4°C. Par comparaison avec des températures estivales du sol de 50°C et plus, il semble vraisemblable que la mortalité nymphale est un facteur important de déclin des populations de L. cuprina au milieu de l'été.