Shirley Pledger

Model‐based approaches to unconstrained ordination

Summary Unconstrained ordination is commonly used in ecology to visualize multivariate data, in particular, to visualize the main trends between different sites in terms of their species composition or relative abundance. Methods of unconstrained ordination currently used, such as non-metric multidimensional scaling, are algorithm-based techniques developed and implemented without directly accommodating the statistical properties of the data at hand. Failure to account for these key data properties can lead to misleading results. A model-based approach to unconstrained ordination can address this issue, and in this study, two types of models for ordination are proposed based on finite mixture models and latent variable models. Each method is capable of handling different data types and different forms of species response to latent gradients. Further strengths of the models are demonstrated via example and simulation. Advantages of model-based approaches to ordination include the following: residual analysis tools for checking assumptions to ensure the fitted model is appropriate for the data; model selection tools to choose the most appropriate model for ordination; methods for formal statistical inference to draw conclusions from the ordination; and improved efficiency, that is model-based ordination better recovers true relationships between sites, when used appropriately.

Support for a rare pattern of temperature-dependent sex determination in archaic reptiles: evidence from two species of tuatara (Sphenodon)

BackgroundThe sex of many reptiles is determined by the temperature an embryo experiences during its development. Three patterns of temperature-dependent sex determination (TSD) have been defined, but one pattern where only males are produced above an upper temperature threshold (Type IB) is controversial. Here we report new data on the relationship between constant temperature incubation and sexual phenotype in two species of tuatara (Sphenodon), archaic reptiles of enormous zoological significance as the sole representatives of a once widespread reptilian order.ResultsIn both species, the pattern observed with constant incubation temperatures from 18 to 23°C (or 24°C) supported a female→male (FM or Type IB) pattern of TSD: in Sphenodon guntheri males were produced above a pivotal temperature of 21.6°C, and in S. punctatus (unnamed subspecies on Stephens Island, Cook Strait), males were produced above a pivotal temperature of 22.0°C. The pivotal temperatures and scaling parameters differed between species (p < 0.001). The thermosensitive period (TSP), where temperature influences gonad morphogenesis, occurs between 0.25 and 0.55 of embryonic development. While it is possible that the more common female→male→female (FMF or Type II) pattern exists, with a second pivotal temperature above 23–24°C, we review several lines of evidence to the contrary. Most notably, we show that in S. punctatus, the warmest natural nests during the TSP produce predominantly males.ConclusionAn FM pattern of TSD could be currently adaptive in promoting sexual size dimorphism in tuatara. However, an FM pattern has particularly serious consequences for S. guntheri because current patterns of global warming could exacerbate the male bias already present in the relic population.

Multivariate methods using mixtures

Matrices of binary or count data are modelled under a unified statistical framework using finite mixtures to group the rows and/or columns. These likelihood-based one-mode and two-mode fuzzy clusterings provide maximum likelihood estimation of parameters and the options of using likelihood ratio tests or information criteria for model comparison. Geometric developments focused on pattern detection give likelihood-based analogues of various techniques in multivariate analysis, including multidimensional scaling, association analysis, ordination, correspondence analysis, and the construction of biplots. Illustrative examples demonstrate the effectiveness of these visualisations for identifying patterns of ecological significance (e.g. abrupt versus slow species turnover).

Size, Growth, and Survival Are Reduced at Cool Incubation Temperatures in the Temperate Lizard Oligosoma suteri (Lacertilia: Scincidae)

Abstract Reptile eggs from cool temperate environments often experience cool incubation conditions, which may have long-term consequences for individual fitness. We studied the effects of artificial incubation regimes on size, growth, and survival of New Zealands only endemic oviparous lizard, Oligosoma suteri. Eggs were randomly distributed among three incubation temperatures (18, 22, 26 C) and two water potentials (−120 and −270 kPa). Hatchlings incubated at 22 C and −120 kPa were significantly larger for most measurements than hatchlings from other incubation treatments. Juveniles from the two higher incubation temperatures had more rapid growth and ultimately greater size by 12 months, as well as significantly higher survival to 18 months, than did 18 C incubated individuals. Hatchling size did not influence survival. Our data suggest that the restricted northern distribution of O. suteri results from ecological constraints caused by the negative effects of cool incubation temperatures on embryos and subsequently hatchlings.

Stopover Duration Analysis with Departure Probability Dependent on Unknown Time Since Arrival

In stopover duration analysis for migratory birds, models with the probability of departure dependent upon time since arrival are useful if the birds are stopping over to replenish body fat. In capture–recapture studies, the exact time of arrival is not generally known, as a bird may not be captured soon after arrival, or it may not be captured at all. We present models which allow for the uncertain knowledge of arrival time, while providing estimates of the total number of birds stopping over, and the distribution and mean of true stopover times for the population.

Egg mass determines hatchling size, and incubation temperature influences post-hatching growth, of tuatara Sphenodon punctatus

The size of reptile hatchlings can be phenotypically plastic in response to incubation temperature, and size is a trait likely to influence fitness – i.e. hatchling size is proposed as an indicator of quality. The parental and incubation temperature effects on the size of one of New Zealands most biologically significant reptile species, the tuatara Sphenodon punctatus are investigated. Artificial incubation at constant temperatures is used to produce founders for new captive and wild populations of tuatara and to augment existing rare populations. We compare size of hatchling tuatara from artificial and natural incubation treatments. The relationship of hatchling size with incubation temperature and sex is examined, and we investigate whether our results support differential fitness models for the evolution of temperature-dependent sex determination in tuatara. Initial egg mass is the most important factor affecting size of hatchling tuatara and is still an important influence at 10 months of age. Incubation temperature does not greatly influence size of hatchlings, but significantly influences size by 10 months of age. Constant artificial incubation conditions result in larger, but possibly less aggressive, juveniles than those from more variable natural incubation conditions by 10 months of age. Evidence from size patterns of tuatara incubated in natural nests supports differential fitness models for the adaptive significance of temperature-dependent sex determination. Thermal variation has little effect on size of male hatchlings, but female embryos that develop in more stable thermal conditions, in more reliable sites for hatching, are bigger and have longer jaws.

Open Capture–Recapture Models with Heterogeneity: II. Jolly–Seber Model

Estimation of abundance is important in both open and closed population capture-recapture analysis, but unmodeled heterogeneity of capture probability leads to negative bias in abundance estimates. This article defines and develops a suite of open population capture-recapture models using finite mixtures to model heterogeneity of capture and survival probabilities. Model comparisons and parameter estimation use likelihood-based methods. A real example is analyzed, and simulations are used to check the main features of the heterogeneous models, especially the quality of estimation of abundance, survival, recruitment, and turnover. The two major advances in this article are the provision of realistic abundance estimates that take account of heterogenetiy of capture, and an appraisal of the amount of overestimation of survival arising from conditioning on the first capture when heterogeneity of survival is present.

Daily Patterns of Metabolic Rate among New Zealand Lizards (Reptilia: Lacertilia: Diplodactylidae and Scincidae)

In addition to the effects of temperature fluctuations on metabolic rate, entrained endogenous rhythms in metabolism, which are independent of temperature fluctuations, may be important in overall energy metabolism in ectotherms. Daily entrained endogenous rhythms may serve as energy‐conserving mechanisms during an animal’s active or inactive phase. However, because nocturnal lizards often take advantage of thermal opportunities during the photophase (light), their daily metabolic rhythms may be less pronounced than those of diurnal species. We measured the rate of oxygen consumption (V̇o2) as an index of metabolic rate of eight temperate lizard species (four nocturnal, three diurnal, and one crepuscular/diurnal; n = 7–14) over 24 h at 13°C and in constant darkness to test whether daily patterns (including amplitude, magnitude, and time of peak V̇o2) of metabolic rate in lizards differ with activity period. We also tested for phylogenetic differences in metabolic rate between skinks and geckos. Three daily patterns were evident: 24‐h cycle, 12‐h cycle, or no daily cycle. The skink Cyclodina aenea has a 12‐h crepuscular pattern of oxygen consumption. In four other species, V̇o2 increased with, or in anticipation of, the active part of the day, but three species had rhythms offset from their active phase. Although not correlated with activity period or phylogeny, amplitude of V̇o2 may be correlated with whether a species is temperate or tropical. In conclusion, the metabolic rate of many species does not always correlate with the recorded activity period. The dichotomy of ecology and physiology may be clarified by more in‐depth studies of species behaviors and activity periods.

The fate of a population of the endemic frog Leiopelma pakeka (Anura: Leiopelmatidae) translocated to restored habitat on Maud Island, New Zealand

Abstract We assess the fate of 100 Leiopelma pakeka transferred in two batches from remnant forest on Maud Island to a new site at Boat Bay, 0.5 km away, in 1984–85. Seventy of the original 100 individual frogs were recaptured, plus 35 young recruits into the population. The 43 frogs released in 1984 settled closer to the release site than did the 57 released a year later, suggesting that many of the later arrivals avoided sites already occupied by frogs. Boat Bay frogs became heavier than frogs in the source population, presumably a reflection of lower population density and greater per capita food supply. Numbers declined initially, but the frog population remained relatively stable after losses of founder individuals began to be offset by local recruitment. The mean annual survival rate after initial settlement was high (97%), indicating an average life expectancy of 33 years.

Plasticity in feeding selectivity and trophic structure of kelp forest associated fishes from northern Chile

Una de las principales formas en que las especies interactuan con su medio ambiente es a traves de la alimentacion, consumiendo directamente una fraccion de los componentes del habitat circundante. El propio habitat, a su vez, puede determinar la conducta de forrajeo y los tipos de alimentacion de sus depredadores. Para investigar la relacion entre la disponibilidad de alimento y la composicion de la dieta de los peces asociados a habitat dominados por macroalgas pardas, se estimo la abundancia de las presas potenciales tanto especies sesiles como moviles y se comparo con la dieta de las especies de los peces en cuatro diferentes sitios de la costa del norte de Chile. Se determino la dieta de los peces y su plasticidad alimentaria mediante la comparacion entre la disponibilidad de presas con los itemes presentes en los estomagos de los peces que fueron capturados por de red de enmalle y arpon de mano. Ademas se calculo el indice de selectividad alfa de Manly y el grado de sobreposicion de la dieta de los peces costeros. Los resultados muestran que la utilizacion de las presas por los depredadores es afectada principalmente por la disponibilidad de presas potenciales. La mayoria de los peces asociados a las macroalgas difieren en su dieta en consonancia con la disponibilidad de los recursos a escalas locales, con la excepcion de dos especies carnivoras tales como Pinguipes chilensis (Valenciennes, 1883) y Paralabrax humeralis (Cuvier & Valenciennes, 1828), cuya dieta no cambio entre los sitios estudiados. Las diferencias en la dieta de las especies son explicadas por los cambios en los recursos bentonicos que varian entre los sitios de estudio. Once de las 12 especies de peces asociados a los bosques de macroalgas pardas mostraron algun grado de selectividad de presas de origen bentonico. Se concluye que la habilidad de los peces de cambiar sus preferencias de alimentacion y, por tanto, la particion de los recursos bentonicos puede obedecer a las adaptaciones para coexistir en un ambiente dinamico como aquel dominado por bosques de macroalgas pardas.