Species distribution models as a tool to estimate reproductive parameters: a case study with a passerine bird species

1.?Correlative species distribution models (SDMs) assess relationships between species distribution data and environmental features, to evaluate the environmental suitability (ES) of a given area for a species, by providing a measure of the probability of presence. If the output of SDMs represents the relationships between habitat features and species performance well, SDM results can be related also to other key parameters of populations, including reproductive parameters. To test this hypothesis, we evaluated whether SDM results can be used as a proxy of reproductive parameters (breeding output, territory size) in red-backed shrikes (Lanius collurio). 2.?The distribution of 726 shrike territories in Northern Italy was obtained through multiple focused surveys; for a subset of pairs, we also measured territory area and number of fledged juveniles. We used Maximum Entropy modelling to build a SDM on the basis of territory distribution. We used generalized least squares and spatial generalized mixed models to relate territory size and number of fledged juveniles to SDM suitability, while controlling for spatial autocorrelation. 3.?Species distribution models predicted shrike distribution very well. Territory size was negatively related to suitability estimated through SDM, while the number of fledglings significantly increased with the suitability of the territory. This was true also when SDM was built using only spatially and temporally independent data. 4.?Results show a clear relationship between ES estimated through presence-only SDMs and two key parameters related to species' reproduction, suggesting that suitability estimated by SDM, and habitat quality determining reproduction parameters in our model system, are correlated. Our study shows the potential use of SDMs to infer important fitness parameters; this information can have great importance in management and conservation.     

Species distribution models as a tool to predict range expansion after reintroduction: A case study on Eurasian beavers (Castor fiber)

Species Distribution Models (SDMs) may provide important information for the follow-up phase of reintroduction operations by identifying the main areas most likely to be colonized by the reintroduced species. We used SDMs to identify the potential distribution of Eurasian beavers (Castor fiber) reintroduced to Serbia and Bosnia and Herzegovina in 2004–2006 after being historically driven to extinction by overhunting. Models were also used to carry out a gap analysis to assess the degree of protection granted by the national reserve networks to the potentially expanding population. Distances from hydrographic network, broadleaved forest, main watercourses and farmland were the main factors influencing model performance. We estimated that suitable habitat covers 14.0% (31,000 km²) of the whole study area. In Serbia, in 2004–2013 beavers expanded their range at a mean colonization speed of 70.9 ± 12.8 km/year (mean ± SD). Only 2.89% of and 9.72% of beaver’s suitable habitat lie within the national network of protected areas of Bosnia and Serbia respectively. We detected new potential areas where beavers will likely settle in the near future, advising on where further monitoring should be carried out. We also identified low suitability areas to be targeted with appropriate management to improve their conditions as well as important regions falling outside reserve boundaries to which protection should be granted.     

Predictive modelling of freshwater fish as a biomonitoring tool in New Zealand

SUMMARY 1. A challenge has been issued to ecologists to find quantitative ecological relationships that have predictive power. A predictive approach has been successful when applied to biomonitoring using stream invertebrates with the River Invertebrate Prediction and Classification System (RIVPACS). This approach, to our knowledge, has not been applied to freshwater fish assemblages.
2. This paper describes the initial results of the application of a regional predictive model of freshwater fish occurrence using 200 reference sites sampled in the Manawatu–Wanganui region of New Zealand over late summer/autumn 2000. In brief (i) sites were classified into biotic groups (ii) the physical and chemical characteristics that best describe variation among these groups were determined and (iii) the relationship between these environmental variables and fish communities was used to predict the fauna expected at a site.
3. Reference sites clustered into six groups based on fish density and community composition. Using 14 physical variables least influenced by human activities, a discriminant model allocated 70% of sites to the correct biological classification group. The variables that best separated the site groups were mainly large-scale variables including altitude, distance from the coast, lotic ecoregion and map co-ordinates.
4. The model was further validated by randomly removing 20% of the sites, rebuilding the model and then determining the number of removed sites correctly allocated to their original biotic groups using environmental variables. Using this process 67% of the removed sites were correctly reassigned to the six predetermined groups.
5. A further 30 sites were used to determine the ability of the model to detect anthropogenic impact. The observed over expected taxa ( O / E ) ratios were significantly lower than the reference site O / E ratios, indicating a response of the fish assemblages to the known stressors.     

Agent-based modelling as scientific method: a case study analysing primate social behaviour

A scientific methodology in general should provide two things: first, a means of explanation and, second, a mechanism for improving that explanation. Agent-based modelling (ABM) is a method that facilitates exploring the collective effects of individual action selection. The explanatory force of the model is the extent to which an observed meta-level phenomenon can be accounted for by the behaviour of its micro-level actors. This article demonstrates that this methodology can be applied to the biological sciences; agent-based models, like any other scientific hypotheses, can be tested, critiqued, generalized or specified. We review the state of the art for ABM as a methodology for biology and then present a case study based on the most widely published agent-based model in the biological sciences: Hemelrijk's DomWorld, a model of primate social behaviour. Our analysis shows some significant discrepancies between this model and the behaviour of the macaques, the genus used for our analysis. We also demonstrate that the model is not fragile: its other results are still valid and can be extended to compensate for these problems. This robustness is a standard advantage of experiment-based artificial intelligence modelling techniques over analytic modelling.     

Fish habitat modelling as a tool for river management

This paper presents an integrated modelling approach to simulate and assess ecological effects of physical habitat changes in rivers. An ecohydraulic simulation tool was created by combining a 1D hydraulic model based on HEC-RAS software and the fish habitat module of CASiMiR, a fuzzy logic-based ecohydraulic modelling system. This tool was applied on a river stretch commonly occurring in Belgium and elsewhere in Europe. In particular the effect of weir removal on habitat suitability for bullhead (Cottus gobio L.) was simulated. Physical conditions of the studied stretch after weir removal were simulated with a hydraulic model. CASiMiR linked these conditions to ecological expert knowledge to calculate habitat suitability for three life stages of bullhead at four different flow rates based on fuzzy logic. Results indicated that after weir removal, habitat suitability increased significantly for all life stages and all flow rates. The presented approach is promising regarding fish community assessment and ecological river engineering.     

Investigating sex‐specific dynamics using uniparental markers: West New Guinea as a case study

Mitochondrial DNA (mtDNA) and Y chromosome (NRY) genetic markers have been often contrasted to investigate sex‐specific dynamics. Traditionally, isolation by distance, intrapopulation genetic diversity and population differentiation are estimated from both markers and compared. Two possible sources of bias are often neglected. First, kilometric distances are frequently used as predictor of the connectivity between groups, hiding the role played by environmental features at a microgeographic scale. Second, the comparison of intrapopulation diversity and population differentiation between mtDNA and NRY is hampered by their different mutational mechanisms and rates. Here, we show how to account for these biases by analyzing from a different perspective a published dataset of eight West New Guinea (WNG) populations for which mtDNA control region sequences and seven linked NRY microsatellites had been typed. First, we modeled the connectivity among sampled populations by computing the number of days required to travel between groups. Then, we investigated the differences between the two sexes accounting for the molecular characteristics of the markers examined to obtain estimates on the product of the effective population size and the migration rate among demes (Nm). We achieved this goal by studying the shape of the gene genealogy at several sampling levels and using spatial explicit simulations. Both the direction and the rate of migration differ between male and females, with an Nm estimated to be >6 times higher in the latter under many evolutionary scenarios. We finally highlight the importance of applying metapopulation models when analyzing the genetic diversity of a species.     

Issues in high-throughput comparative modelling: a case study using the ubiquitin E2 conjugating enzymes

Sequences of the ubiquitin-conjugating enzyme (UBC or E2) family were used as a test set to investigate issues associated with the high-throughput comparative modelling of protein structures. A semi-automatic method was initially developed with particular emphasis on producing models of a quality suitable for structural comparison. Structural and sequence features of the E2 family were used to improve the sequence alignment and the quality of the structural templates. Initially, failure to correct for subtle structural inconsistencies between templates lead to problems in the comparative analysis of the UBC electrostatic potentials. Modelling of known UBC structures using Modeller 4.0 showed that multiple templates produced, on average, no better models than the use of just one template, as judged by the root-mean-squared deviation between the comparative model and crystal structure backbones. Using four different quality-checking methods, for a given target sequence, it was not possible to distinguish the model most similar to the experimental structure. The UBC models were thus finally modelled using only the crystal structure template with the highest sequence identity to the target to be modelled, and producing only one model solution. Quality checking was used to reject models with obvious structural anomalies (e.g., bad side-chain packing). The resulting models have been used for a comparison of UBC structural features and of their electrostatic potentials. The work was extended through the development of a fully automated pipeline that identifies E2 sequences in the sequence databases, aligns and models them, and calculates the associated electrostatic potential.     

Multiscale modelling as a tool to prescribe realistic boundary conditions for the study of surgical procedures

This work was motivated by the problems of analysing detailed 3D models of vascular districts with complex anatomy. It suggests an approach to prescribing realistic boundary conditions to use in order to obtain information on local as well as global haemodynamics. A method was developed which simultaneously solves Navier-Stokes equations for local information and a non-linear system of ordinary differential equations for global information. This is based on the principle that an anatomically detailed 3D model of a cardiovascular district can be achieved by using the finite element method. In turn the finite element method requires a specific boundary condition set. The approach outlined in this work is to include the system of ordinary differential equations in the boundary condition set. Such a multiscale approach was first applied to two controls: (i) a 3D model of a straight tube in a simple hydraulic network and (ii) a 3D model of a straight coronary vessel in a lumped-parameter model of the cardiovascular system. The results obtained are very close to the solutions available for the pipe geometry. This paper also presents preliminary results from the application of the methodology to a particular haemodynamic problem: namely the fluid dynamics of a systemic-to-pulmonary shunt in paediatric cardiac surgery.     

Influence of device accuracy and choice of algorithm for species distribution modelling of seabirds: a case study using black‐browed albatrosses

Species distribution models (SDM) based on tracking data from different devices are used increasingly to explain and predict seabird distributions. However, different tracking methods provide different data resolutions, ranging from < 10 m to > 100 km. To better understand the implications of this variation, we modeled the potential distribution of black‐browed albatrosses Thalassarche melanophris from South Georgia that were simultaneously equipped with a platform terminal transmitter (PTT) (high resolution) and a global location sensor (GLS) logger (coarse resolution), and measured the overlap of the respective potential distribution for a total of nine different SDM algorithms. We found slightly better model fits for the PTT than for GLS data (AUC values 0.958 ± 0.048 vs 0.95 ± 0.05) across all algorithms. The overlaps of the predicted distributions were higher between device types for the same algorithm, than among algorithms for either device type. Uncertainty arising from coarse‐resolution location data is therefore lower than that associated with the modeling technique. Consequently, the choice of an appropriate algorithm appears to be more important than device type when applying SDMs to seabird tracking data. Despite their low accuracy, GLS data appear to be effective for analyzing the habitat preferences and distribution patterns of pelagic species.     

Using induced pluripotent stem cells as a tool for modelling carcinogenesis

Cancer is a highly heterogeneous group of diseases that despite improved treatments remain prevalent accounting for over 14 million new cases and 8.2 million deaths per year. Studies into the process of carcinogenesis are limited by lack of appropriate models for the development and pathogenesis of the disease based on human tissues. Primary culture of patient samples can help but is difficult to grow for a number of tissues. A potential opportunity to overcome these barriers is based on the landmark study by Yamanaka which demonstrated the ability of four factors;Oct4, Sox2, Klf4, and c-Myc to reprogram human somatic cells in to pluripotency. These cells were termed induced pluripotent stem cells(i PSCs) and display characteristic properties of embryonic stem cells. This technique has a wide range of potential uses including disease modelling, drug testing and transplantation studies. Interestingly i PSCs also share a number of characteristics with cancer cells including self-renewal and proliferation, expression of stem cell markers and altered metabolism. Recently, i PSCs have been generated from a number of human cancer cell lines and primary tumour samples from a range of cancers in an attempt to recapitulate the development of cancer and interrogate the underlying mechanisms involved. This review will outline the similarities between the reprogramming process and carcinogenesis, and how these similarities have been exploited to generate i PSC models for a number of cancers.     

Pressure as a tool to study protein-unfolding/refolding processes: the case of ribonuclease A

This paper gives an overview of the application of high-pressure to study the folding/unfolding processes of proteins using Ribonuclease A as a model protein. A particular focus is the study of pressure-equilibrium unfolding and folding kinetics using variants and the information obtained by comparing these with the wild-type enzyme.     

Species distribution modelling in low‐interaction environments: Insights from a terrestrial Antarctic system

It is widely acknowledged that in the terrestrial Antarctic, interspecific interactions are typically unimportant in determining species distributions and community structure. Therefore, correlative models should prove useful for predicting current and future spatial variation in species abundance patterns. However, this idea has not been formally tested, and the utility of such models, which have shown value for understanding the distribution of diversity elsewhere, for investigating biodiversity patterns in Antarctica remains unclear. Here we make a start at such tests by using generalized linear and simultaneous autoregressive models to demonstrate that simple environmental variables and information about the spatial structure of the environment can explain more than 90% of the variation in the abundance of Maudheimia wilsoni (Oribatida; Maudheimiidae), a representative of one of the most significant groups of Antarctic terrestrial arthropods, the mites. We show that a single environmental variable, maximum soil moisture content, can account for as much as 80% of the variance in the abundance of the mite, and that linear models with only a few environmental and spatial terms can be used to forecast the species abundance at the landscape scale. Given ongoing calls for better understanding of the distribution of Antarctic diversity and its likely future change, this initial test indicates that such modelling procedures, and more sophisticated versions thereof, hold much promise for the region and should be tested for other taxa with different life forms and habitat requirements.     

The influence of spatial resolution on macroecological patterns of range size variation: a case study using parrots (Aves: Psittaciformes) of the world

Aim To assess the extent to which the resolution at which geographical range sizes are measured influences macroecological patterns in this variable. Location Global. Methods Data on the geographical ranges of parrot species were digitized, and a Geographic Information System used to produce nine range size estimates for each species using different degrees of spatial resolution. The inter‐correlation of these estimates was then compared, together with their patterns of covariation with population size, body mass and migratory behaviour (across species and controlling for phylogeny), their pattern of phylogenetic correlation, and the frequency distributions of the different measures. Results Strong correlations exist among all nine range size measures across species, albeit that measures of similar spatial resolution are more strongly correlated. All measures show similar patterns of covariation with population size, body mass and migratory behaviour, and similar patterns of phylogenetic correlation. The skewness of frequency distributions increases towards zero as the resolution of the range size measure declines. Main conclusions The results of macroecological analyses are little affected by the resolution with which geographical range sizes are calculated, at least for the parrots of the world. Previously published studies based on crude measures of range size would be unlikely to have produced markedly different conclusions had they used more refined range size metrics.