Augmenting superpopulation capture-recapture models with population assignment data

Summary Ecologists applying capture–recapture models to animal populations sometimes have access to additional information about individuals' populations of origin (e.g., information about genetics, stable isotopes, etc.). Tests that assign an individual's genotype to its most likely source population are increasingly used. Here we show how to augment a superpopulation capture–recapture model with such information. We consider a single superpopulation model without age structure, and split each entry probability into separate components due to births in situ and immigration. We show that it is possible to estimate these two probabilities separately. We first consider the case of perfect information about population of origin, where we can distinguish individuals born in situ from immigrants with certainty. Then we consider the more realistic case of imperfect information, where we use genetic or other information to assign probabilities to each individual's origin as in situ or outside the population. We use a resampling approach to impute the true population of origin from imperfect assignment information. The integration of data on population of origin with capture–recapture data allows us to determine the contributions of immigration and in situ reproduction to the growth of the population, an issue of importance to ecologists. We illustrate our new models with capture–recapture and genetic assignment data from a population of banner‐tailed kangaroo rats Dipodomys spectabilis in Arizona.     

Environmental data sets matter in ecological niche modelling: an example with Solenopsis invicta and Solenopsis richteri

Aim  In response to a recent paper suggesting the failure of ecological niche models to predict between native and introduced distributional areas of fire ants ( Solenopsis invicta ), we sought to assess methodological causes of this failure.
Location  Ecological niche models were developed on the species' native distributional area in South America, and projected globally.
Methods  We developed ecological niche models based on six different environmental data sets, and compared their respective abilities to anticipate the North American invasive distributional area of the species.
Results  We show that models based on the 'bioclimatic variables' of the WorldClim data set indeed fail to predict the full invasive potential of the species, but that models based on four other data sets could predict this potential correctly.
Main conclusions  The difference in predictive abilities appears to centre on the complexity of the environmental variables involved. These results emphasize important influences of environmental data sets on the generality and ability of ecological niche models to anticipate novel phenomena, and offer a simpler explanation for the lack of predictive ability among native and invaded distributional areas than that of niche shifts.     

Multievent: an extension of multistate capture-recapture models to uncertain states

Capture-recapture models were originally developed to account for encounter probabilities that are less than 1 in free-ranging animal populations. Nowadays, these models can deal with the movement of animals between different locations and are also used to study transitions between different states. However, their use to estimate transitions between states does not account for uncertainty in state assignment. I present the extension of multievent models, which does incorporate this uncertainty. Multievent models belong to the family of hidden Markov models. I also show in this article that the memory model, in which the next state or location is influenced by the previous state occupied, can be fully treated within the framework of multievent models.     

Refugia,colonization and diversification of an arid‐adapted bird: coincident patterns between genetic data and ecological niche modelling

Phylogeographical studies are common in boreal and temperate species from the Palaearctic, but scarce in arid‐adapted species. We used nuclear and mitochondrial markers to investigate phylogeography and to estimate chronology of colonization events of the trumpeter finch Bucanetes githagineus, an arid‐adapted bird. We used 271 samples from 16 populations, most of which were fresh samples but including some museum specimens. Microsatellite data showed no clear grouping according to the sampling locations. Microsatellite and mitochondrial data showed the clearest differentiation between Maghreb and Canary Islands and between Maghreb and Western Sahara. Mitochondrial data suggest differentiation between different Maghreb populations and among Maghreb and Near East populations, between Iberian Peninsula and Canary Islands, as well as between Western Sahara and Maghreb. Our coalescence analyses indicate that the trumpeter finch colonized North Africa during the humid Marine Isotope Stage 5 (MIS5) period of the Sahara region 125 000 years ago. We constructed an ecological niche model (ENM) to estimate the geographical distribution of climatically suitable habitats for the trumpeter finch. We tested whether changes in the species range in relation to glacial–interglacial cycles could be responsible for observed patterns of genetic diversity and structure. Modelling results matched with those from genetic data as the species' potential range increases in interglacial scenarios (in the present climatic scenario and during MIS5) and decreases in glacial climates (during the last glacial maximum, LGM, 21 000 years ago). Our results suggest that the trumpeter finch responded to Pleistocene climatic changes by expanding and contracting its range.     

Local survival after fire in Mediterranean shrublands: combining capture-recapture data over several bird species

Post-disturbance survival is a key factor in the onset of secondary successions. Here we analyse capture-recapture data from two before/after disturbance studies to estimate the effect of fire on local bird survival. Analyses of six bird species at two Mediterranean shrubland sites were combined using a meta-analysis approach. Two warblers, Sylvia undata and S. melanocephala, were studied at one site altered by prescribed burning, and five passerines (Luscinia megarhynchos, Turdus merula, Parus major, P. caeruleus and S. melanocephala) at one site disturbed by wildfire. Based on the combined analysis, annual survival probability significantly decreased from 0.49 to 0.18 (i.e. a 64% decline) after the fire. Our results further suggest a trend for a higher decrease in annual survival associated with wildfire (–72%, from 0.51 to 0.14) than with prescribed burning (–35%, from 0.41 to 0.27), although this should be properly tested with a specific experimental design. In S. undata, a decline in survival in the long-term cannot account for the drop in density observed the first spring after fire. We suggest that a decrease in recruitment rate and an increase in the proportion of non-breeders immediately after the fire may contribute more strongly to the decline in the breeding population. Our results tend to support the idea that bird populations may respond to moderate disturbances with noticeable time lags, because of individual site tenacity.     

On valuing patches: estimating contributions to metapopulation growth with reverse-time capture-recapture modelling

Metapopulation ecology has historically been rich in theory, yet analytical approaches for inferring demographic relationships among local populations have been few. We show how reverse-time multi-state capture-recapture models can be used to estimate the importance of local recruitment and interpopulation dispersal to metapopulation growth. We use 'contribution metrics' to infer demographic connectedness among eight local populations of banner-tailed kangaroo rats, to assess their demographic closure, and to investigate sources of variation in these contributions. Using a 7 year dataset, we show that: (i) local populations are relatively independent demographically, and contributions to local population growth via dispersal within the system decline with distance; (ii) growth contributions via local survival and recruitment are greater for adults than juveniles, while contributions involving dispersal are greater for juveniles; (iii) central populations rely more on local recruitment and survival than peripheral populations; (iv) contributions involving dispersal are not clearly related to overall metapopulation density; and (v) estimated contributions from outside the system are unexpectedly large. Our analytical framework can classify metapopulations on a continuum between demographic independence and panmixia, detect hidden population growth contributions, and make inference about other population linkage forms, including rescue effects and source-sink structures. Finally, we discuss differences between demographic and genetic population linkage patterns for our system.     

Relative importance of factors controlling the success of Oxalis acetosella: an example of linear modelling in ecological research

An ecological hypothesis concerning the relative importance of factors governing the success of Oxalis acetosella on mesic upland forest sites in southern Finland was formulated and tested statistically by means of a multivariate linear model. The data consisted of a stratified random sample of 40 plots with biological measurements and associated observations on environmental variables. The covariance matrix between the incorporated variables was computed and the model parameters were estimated using the method of maximum likelihood provided by the computer programme LISREL V. The results supported the hypothesis based on previous observations and experiments: Oxalis acetosella benefits from a high nutrient level of the soil, but is decisively dependent on the shelter provided by the tree stand. When both spruce stands and well-lit pine stands on mesic and relatively rich forest sites were considered simultaneously, only a weak correlation was found between light availability and site fertility. Accordingly, the presumed value of Oxalis acetosella as an indicator of site fertility appears to be questionable. The adequacy of linear modelling in an ecological context is discussed. The kind of models applied in this study have only a limited application range in non-experimental ecological research. However, linear modelling may contribute to solving particular ecological problems in cases where short environmental gradients are considered so that nonlinearity is not a dominant feature.     

Diet of stone martens: an example of ecological flexibility

The feeding ecology of the stone marten in a rural area of Central Italy was assessed by faecal analysis. Habitat analysis, performed through a Geographical Information System, and intensive radio-tracking allowed us to investigate intra-population variations of diet in relation to habitat. The species'feeding habits were opportunistic: fruit and berries were the staple diet but mammals and birds were also important. Diet varied seasonally in relation to resource availability, with a predominance of fruit in autumn and frequent presence of insects in summer. Individuals living in adjacent areas but in different habitats (wooded and rural) showed significant variations of diet, adapting their feeding habits to local availability of foods. The great adaptability of the stone marten to very different resource conditions can represent a key to the species'success through its wide range.     

PhosphoScore: an open-source phosphorylation site assignment tool for MSn data

Correct phosphorylation site assignment is a critical aspect of phosphoproteomic analysis. Large-scale phosphopeptide data sets that are generated through liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) analysis often contain hundreds or thousands of phosphorylation sites that require validation. To this end, we have created PhosphoScore, an open-source assignment program that is compatible with phosphopeptide data from multiple MS levels (MS(n)). The algorithm takes into account both the match quality and normalized intensity of observed spectral peaks compared to a theoretical spectrum. PhosphoScore produced >95% correct MS(2) assignments from known synthetic data, > 98% agreement with an established MS(2) assignment algorithm (Ascore), and >92% agreement with visual inspection of MS(3) and MS(4) spectra.     

Epidemic predictions in an imperfect world: modelling disease spread with partial data

‘Big-data’ epidemic models are being increasingly used to influence government policy to help with control and eradication of infectious diseases. In the case of livestock, detailed movement records have been used to parametrize realistic transmission models. While livestock movement data are readily available in the UK and other countries in the EU, in many countries around the world, such detailed data are not available. By using a comprehensive database of the UK cattle trade network, we implement various sampling strategies to determine the quantity of network data required to give accurate epidemiological predictions. It is found that by targeting nodes with the highest number of movements, accurate predictions on the size and spatial spread of epidemics can be made. This work has implications for countries such as the USA, where access to data is limited, and developing countries that may lack the resources to collect a full dataset on livestock movements.     

From sensor data to animal behaviour: an oystercatcher example

Animal-borne sensors enable researchers to remotely track animals, their physiological state and body movements. Accelerometers, for example, have been used in several studies to measure body movement, posture, and energy expenditure, although predominantly in marine animals. In many studies, behaviour is often inferred from expert interpretation of sensor data and not validated with direct observations of the animal. The aim of this study was to derive models that could be used to classify oystercatcher (Haematopus ostralegus) behaviour based on sensor data. We measured the location, speed, and tri-axial acceleration of three oystercatchers using a flexible GPS tracking system and conducted simultaneous visual observations of the behaviour of these birds in their natural environment. We then used these data to develop three supervised classification trees of behaviour and finally applied one of the models to calculate time-activity budgets. The model based on accelerometer data developed to classify three behaviours (fly, terrestrial locomotion, and no movement) was much more accurate (cross-validation error?=?0.14) than the model based on GPS-speed alone (cross-validation error?=?0.35). The most parsimonious acceleration model designed to classify eight behaviours could distinguish five: fly, forage, body care, stand, and sit (cross-validation error?=?0.28); other behaviours that were observed, such as aggression or handling of prey, could not be distinguished. Model limitations and potential improvements are discussed. The workflow design presented in this study can facilitate model development, be adapted to a wide range of species, and together with the appropriate measurements, can foster the study of behaviour and habitat use of free living animals throughout their annual routine.     

生态足迹方法:可持续性定量研究的新方法——以张掖地区1995年的生态足迹计算为例

生态足迹是一种定量测量人类对自然利用程度的新方法。通过跟踪区域的能源和资源消费,将它们转化为提供这种物质流所必须的各种生物生产型土地类型的面积,并同区域能提供的生物生产型土地面积进行比较,能定量判断一个区域的发展是否处于生态承载能力的范围内,介绍了生态足迹的概念及生态足迹计算模型,分析总结了生态足迹模型的优缺点等,在此基础上,对张掖地区1995年生态足迹进行了实证计算和分析,结果表明1995年张掖地区人均生态字为0．34hm^2.     

Floating stereospecific assignment revisited: Application to an 18 kDa protein and comparison with J-coupling data

We report a floating chirality procedure to treat nonstereospecifically assigned methylene orisopropyl groups in the calculation of protein structures from NMR data using restrainedmolecular dynamics and simulated annealing. The protocol makes use of two strategies toinduce the proper conformation of the prochiral centres: explicit atom swapping followingan evaluation of the NOE energy term, and atom floating by reducing the angle andimproper force constants that enforce a defined chirality at the prochiral centre. The individualcontributions of both approaches have been investigated. In addition, the effects of accuracyand precision of the interproton distance restraints were studied. The model system employedis the 18 kDa single-stranded DNA binding protein encoded by Pseudomonas bacteriophagePf3. Floating chirality was applied to all methylene and isopropyl groups that give rise to non-degenerate NMR signals, and the results for 34 of these groups were compared to J-couplingdata. We conclude that floating stereospecific assignment is a reliable tool in protein structurecalculation. Its use is beneficial because it allows the distance restraints to be extracteddirectly from the measured peak volumes without the need for averaging or addingpseudoatom corrections. As a result, the calculated structures are of a quality almostcomparable to that obtained with stereospecific assignments. As floating chirality furthermoreis the only approach treating prochiral centres that ensures a consistent assignment of the twoproton frequencies in a single structure, it seems to be preferable over using pseudoatoms or(R-6) averaging.     

Deriving ecological relationships from geographical correlations between host and parasitic species: an example with orchid bees

Aim  To investigate biogeographical patterns of cleptoparasitic Exaerete bee species and their orchid bee hosts.
Location  Neotropical region, from Central America to southern Brazil.
Methods  Correlations between relative frequencies of cleptoparasitic Exaerete species and their host Eulaema species were employed to investigate the geographical association between such species pairs.
Results  Our data support the current proposition that the Eulaema meriana / Eulaema flavescens complex is the main host for Exaerete frontalis . Contrary to current belief, however, Eulaema nigrita apparently is not the only and, in some regions, not the most important host for Exaerete smaragdina .
Main conclusions  Current knowledge on cleptoparasite host associations among orchid bees is based on fortuitous observations, and in some instances generalizations from such observations are not corroborated by the frequencies and distributions of the bees involved. Our data suggest that cleptoparasitic pressure, rather than other features of the forest environment, may be responsible for the low abundance of E. nigrita in the Amazonian forests.     

Developing an index of wetland condition from ecological data: An example using HGM functional variables from the Nanticoke watershed,USA

Demand for data on the ecological condition of wetlands is increasing as state and federal management programs recognize its value in reporting on the ambient condition of the resource, targeting restoration and protection efforts, evaluating the effects of mitigation and restoration practices, supporting regulatory decisions, and tracking the impact of land use decisions. We developed an approach for generating a single measure of wetland condition from ecological variables used in hydrogeomorphic (HGM) assessment. An Index of Wetland Condition (IWC) was developed from HGM field data collected to assess freshwater, non-tidal flat, riverine, and depression wetlands in the Nanticoke River watershed. The HGM variables were screened and scored based on a range check, responsiveness, and metric redundancy, employing a method used to develop indices of biotic integrity. Weights of the individual variables were adjusted to reflect our understanding of wetland ecology and to include variables that represented the vegetation, hydrology, and buffer of a wetland. The final IWC score discriminated high, medium, and low site disturbance classes in flat and riverine wetlands and high and low disturbance classes in depressions, one-way ANOVA F-values ranged from 44.5 to 79.1 (all p <0.0001). The combination of the IWC and HGM assessments provides a comprehensive evaluation of the wetland resource. HGM produces information on specific wetland functions. The IWC concisely conveys the ecological condition of the resource and maximizes the utility of the data collected in an HGM assessment.     

Updating bird species distribution at large spatial scales: applications of habitat modelling to data from long-term monitoring programs

Mapping of species distributions at large spatial scales has been often based on the representation of gathered observations in a general grid atlas framework. More recently, subsampling and subsequent interpolation or habitat spatial modelling techniques have been incorporated in these projects to allow more detailed species mapping. Here, we explore the usefulness of data from long-term monitoring (LTM) projects, primarily aimed at estimating trends in species abundance and collected at shorter time intervals (usually yearly) than atlas data, to develop predictive habitat models. We modelled habitat occupancy for 99 species using a bird LTM program and evaluated the predictive accuracy of these models using independent data from a contemporary and comprehensive breeding bird atlas project from the same region. Habitat models from LTM data using generalized linear modelling were significant for all the species and generally showed a high predictive power, albeit lower than that from atlas models. Sample size and species range size and niche breadth were the most important factors behind variability in model predictive accuracy, whereas the spatial distribution of sampling units at a given sample size had minor effects. Although predictive accuracy of habitat modelling was strongly species dependent, increases in sample size and, secondarily, a better spatial distribution of sampling units should lead to more powerful predictive distribution models. We suggest that data from LTM programs, now established in a large number of countries, has the potential for being a major source of good quality data suitable for the estimation and regularly update of distributions at large spatial scales for a number of species.