Are the numbers adding up? Exploiting discrepancies among complementary population models

Large carnivores are difficult to monitor because they tend to be sparsely distributed, sensitive to human activity, and associated with complex life histories. Consequently, understanding population trend and viability requires conservationists to cope with uncertainty and bias in population data. Joint analysis of combined data sets using multiple models (i.e., integrated population model) can improve inference about mechanisms (e.g., habitat heterogeneity and food distribution) affecting population dynamics. However, unobserved or unobservable processes can also introduce bias and can be difficult to quantify. We developed a Bayesian hierarchical modeling approach for inference on an integrated population model that reconciles annual population counts with recruitment and survival data (i.e., demographic processes). Our modeling framework is flexible and enables a realistic form of population dynamics by fitting separate density-dependent responses for each demographic process. Discrepancies estimated from shared parameters among different model components represent unobserved additions (i.e., recruitment or immigration) or removals (i.e., death or emigration) when annual population counts are reliable. In a case study of gray wolves in Wisconsin (1980–2011), concordant with policy changes, we estimated that a discrepancy of 0% (1980–1995), −2% (1996–2002), and 4% (2003–2011) in the annual mortality rate was needed to explain annual growth rate. Additional mortality in 2003–2011 may reflect density-dependent mechanisms, changes in illegal killing with shifts in wolf management, and nonindependent censoring in survival data. Integrated population models provide insights into unobserved or unobservable processes by quantifying discrepancies among data sets. Our modeling approach is generalizable to many population analysis needs and allows for identifying dynamic differences due to external drivers, such as management or policy changes.     

Basking Activity is Modulated by Health State but is Constrained by Conspicuousness to Predators in Male Spanish Terrapins

Aerial basking may have several benefits for freshwater turtles in addition to thermoregulation such as removing parasites from the skin, which would improve health state. However, basking outside of water may be risky because it may expose freshwater turtles to terrestrial predators. Here, we monitored the basking activity of male Spanish terrapins (Mauremys leprosa) in a wild population of the south‐western of the Iberian Peninsula. We also measured body size, health state parameters, parasite prevalence, and limb coloration of these individuals. We aimed to examine whether basking may improve health state of turtles. The results showed that male turtles with higher basking activity were those parasitized by Hepatozoon and that had lower total white blood cell (WBC). This might indicate that turtles in worse health condition increase their time spent basking to improve their immune system. In addition, because basking might be risky, we also expected that turtles with more conspicuous coloration should reduce their basking activity to avoid being detected by potential predators. We found that infected turtles, but not uninfected ones, that spent more time basking also had less bright coloration in limb stripes. Our study provides evidence that basking activity may improve health state of terrapins, but that color conspicuity may increase costs of basking, especially for parasitized individuals. Understanding the balance between the benefits and the costs of basking might be essential for the conservation of freshwater turtle populations.     

Extant Lizard Tracks: Variation and Implications for Paleoichnology

In this study, I collected tracks and trackways from nine species of extant lizards representing all five major lizard clades. Previously, tracks from species of only two of these clades were described. Lizard tracks conventionally are regarded as having curved digit imprints that progressively increase in length from digit I to IV, with a smaller digit V directing antero-laterally. However, the zygodactylous feet of chameleons (Calumma parsonii and Furcifer pardalis), the posteriorly directed digit V in the pes of ground-dwelling geckos (Eublepharis macularius) and the rounded feet of blue-tongued skinks (Tiliqua scincoides) did not make “typical” lizard tracks, and demonstrate that even within a limited taxonomic sample there can be considerable variation in the morphologies of lizard tracks. Among the lizards examined, mode of locomotion and how the feet function have more influence on the morphology of tracks than does the phylogenetic affinities of the trackmaker. This preliminary neoichnological study increases the known variation in lizard tracks and aids in interpreting the fossil trackway record by providing comparative information that can be used to identify fossil tracks made by lizards.     

New Ichnotaxa of Mammal and Reptile Tracks from the Upper Paleocene of Alberta

Only two vertebrate trackways are known from the Paleocene of western Canada and are among the few Paleocene vertebrate trackways known worldwide.

A natural cast trackway consisting of five prints (three pes, two manus) on a fallen block was found along the Red Deer River, near the town of Red Deer, Alberta, in 1927. The discoverers, Ralph Rutherford and Loris Russell, identified the strata the track block had fallen from as belonging to the Paskapoo Formation (upper Paleocene: middle Tiffanian). The trackway was attributed to a mammalian track-maker in two subsequent publications. However, the prints are more characteristic of a reptilian (crocodylian) track-maker.

A natural cast track-bearing block was discovered on Signal Hill in the city of Calgary during the preparation of a new residential subdivision in 1990. The large track-bearing block was found in a rock pile but is suspected to have originated from strata belonging to the Porcupine Hills Formation (Upper Paleocene: late Torrejonian), which was being excavated at the time. This large slab contains twelve prints (six pes, six manus) and is associated with extensive mud cracks. The mammalian affinity of the trackmaker was recognized by researchers from the Royal Tyrrell Museum of Palaeontology.     

Trackway Ratio: A New Look at Trackway Gauge in the Analysis of Quadrupedal Dinosaur Trackways and its Implications for Ichnotaxonomy

A new parameter, the Trackway Ratio (TR), is proposed to supplement the previously used trackway gauge to describe and quantify the relative width of trackways in dinosaur quadrupedal gaits. It is expressed as the ratio of the width of the tracks relative to the total width of the trackway (both measured perpendicular to the long axis of the trackway). The ratio may be used with either pes (PTR) or manus (MTR) tracks. The PTR range of values for wide-, medium- and narrow-gauge trackways of previous authors are provisionally suggested to be ≤35%, 36–49% and ≥50%, respectively. The application of such a ratio would permit a more consistent ichnotaxonomy to be adopted where both track morphology and trackway parameters are used to define ichnotaxa.

Determination of the TR, as well as other parameters, will be affected by track preservation quality. Recent experiments on track simulation in the laboratory have shed further light on observations made in the field concerning the value of track measurements (in particular track length and width) recorded from below the surface on which the maker was moving. Experimental track simulations in the laboratory have shown that the dimensions of transmitted tracks preserved below the surface on which the foot was impressed may vary from 65% to 135% of the true dimensions of the indenter. Two case studies are presented that quantify the errors that may be made on calculating TR and the size, gait and speed of the maker, from trackways if the preservation of the tracks are not fully understood.

It is shown that in individual trackways the PTR may vary along the length of the trackway; so that part of the trackway may be classified as wide-gauge and other parts medium-gauge. There is a relationship between variation in PTR and that of pace angulation along the length of a single trackway. An analysis of 42 trackways, principally sauropod, shows a temporal distribution that does not agree closely with previous suggestions relating to narrow- and wide-gauge trackways.     

Abacus: a computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis

We describe Abacus, a computational tool for extracting spectral counts from MS/MS data sets. The program aggregates data from multiple experiments, adjusts spectral counts to accurately account for peptides shared across multiple proteins, and performs common normalization steps. It can also output the spectral count data at the gene level, thus simplifying the integration and comparison between gene and protein expression data. Abacus is compatible with the widely used Trans-Proteomic Pipeline suite of tools and comes with a graphical user interface making it easy to interact with the program. The main aim of Abacus is to streamline the analysis of spectral count data by providing an automated, easy to use solution for extracting this information from proteomic data sets for subsequent, more sophisticated statistical analysis.     

Shotgun proteomic analysis for detecting differentially expressed proteins in the reduced culm number rice

To survey protein expression patterns in the reduced culm number (RCN) rice, a comparative shotgun proteomic analysis was conducted. For large-scale protein identification, multidimensional protein identification technology (MudPIT) coupled with pre-fractionation of plant shoot proteins led to the identification of 3004 non-redundant rice proteins. By statistically comparing relative amounts of 1353 reproducibly identified proteins between the RCN rice and the wild-type rice, 44 differentially expressed proteins were detected, where 42 proteins were increased and 2 proteins were decreased in the RCN rice. These proteins appear to have roles in glycolysis, trichloroacetic acid cycle, secondary metabolism, nutrient recycling, and nucleotide metabolism and repair. Consequently, we hypothesized that the RCN rice might fail to maintain sugar nutrient homeostasis. This was confirmed with the observation that the sucrose concentration was increased significantly in the RCN rice compared with the wild-type rice. Also, the RCN rice showed a hypersensitive response to exogenous sucrose treatment.     

The New Zealand Scincidae (Reptilia: Lacertilia); a taxonomic and zoogeographic study

Abstract

The mohua (or yellowhead, Mohoua ochrocephala) is an endangered hole‐nesting passerine which is now absent from >75% of its former range. This paper describes an 11 year monitoring programme, which was set up to survey 14 populations at 12 key sites throughout the range of the mohua, in order to document the pattern of population change and provide early warning of likely local extinctions. Between 1983 and 1993, one mohua population became extinct. Five of the 14 populations declined significantly, and three of these were on the verge of extinction by 1993. One population increased, and seven did not change significantly, although a declining trend was recorded at five of these. Six population crashes coincided with irruptions of stoats (Mustela erminea) following heavy beech (Nothofagus) seeding.     

Models for Estimating Abundance from Repeated Counts of an Open Metapopulation

Summary Using only spatially and temporally replicated point counts, Royle (2004b, Biometrics 60, 108–115) developed an N ‐mixture model to estimate the abundance of an animal population when individual animal detection probability is unknown. One assumption inherent in this model is that the animal populations at each sampled location are closed with respect to migration, births, and deaths throughout the study. In the past this has been verified solely by biological arguments related to the study design as no statistical verification was available. In this article, we propose a generalization of the N ‐mixture model that can be used to formally test the closure assumption. Additionally, when applied to an open metapopulation, the generalized model provides estimates of population dynamics parameters and yields abundance estimates that account for imperfect detection probability and do not require the closure assumption. A simulation study shows these abundance estimates are less biased than the abundance estimate obtained from the original N ‐mixture model. The proposed model is then applied to two data sets of avian point counts. The first example demonstrates the closure test on a single‐season study of Mallards (Anas platyrhynchos), and the second uses the proposed model to estimate the population dynamics parameters and yearly abundance of American robins (Turdus migratorius) from a multi‐year study.