Applying species distribution modelling to identify areas of high conservation value for endangered species: A case study using Margaritifera margaritifera (L.)

The development and implementation of a population supplementation and restoration plan for any endangered species should involve an understanding of the species’ habitat requirements prior to the release of any captive bred individuals. The freshwater pearl mussel, Margaritifera margaritifera, has undergone dramatic declines over the last century and is now globally endangered. In Northern Ireland, the release of captive bred individuals is being used to support wild populations and repatriate the species in areas where it once existed. We employed a combination of maximum entropy modelling (MAXENT) and Generalized Linear Mixed Models (GLMM) to identify ecological parameters necessary to support wild populations using GIS-based landscape scale and ground-truthed habitat scale environmental parameters. The GIS-based landscape scale model suggested that mussel occurrence was associated with altitude and soil characteristics including the carbon, clay, sand, and silt content. Notably, mussels were associated with a relatively narrow band of variance indicating that M. margaritifera has a highly specific landscape niche. The ground-truthed habitat scale model suggested that mussel occurrence was associated with stable consolidated substrates, the extent of bankside trees, presence of indicative macrophyte species and fast flowing water. We propose a three phase conservation strategy for M. margaritifera identifying suitable areas within rivers that (i) have a high conservation value yet needing habitat restoration at a local level, (ii) sites for population supplementation of existing populations and (iii) sites for species reintroduction to rivers where the mussel historically occurred but is now locally extinct. A combined analytical approach including GIS-based landscape scale and ground-truthed habitat scale models provides a robust method by which suitable release sites can be identified for the population supplementation and restoration of an endangered species. Our results will be highly influential in the future management of M. margaritifera in Northern Ireland.

Incorporating uncertainty in predictive species distribution modelling

Motivated by the need to solve ecological problems (climate change, habitat fragmentation and biological invasions), there has been increasing interest in species distribution models (SDMs). Predictions from these models inform conservation policy, invasive species management and disease-control measures. However, predictions are subject to uncertainty, the degree and source of which is often unrecognized. Here, we review the SDM literature in the context of uncertainty, focusing on three main classes of SDM: niche-based models, demographic models and process-based models. We identify sources of uncertainty for each class and discuss how uncertainty can be minimized or included in the modelling process to give realistic measures of confidence around predictions. Because this has typically not been performed, we conclude that uncertainty in SDMs has often been underestimated and a false precision assigned to predictions of geographical distribution. We identify areas where development of new statistical tools will improve predictions from distribution models, notably the development of hierarchical models that link different types of distribution model and their attendant uncertainties across spatial scales. Finally, we discuss the need to develop more defensible methods for assessing predictive performance, quantifying model goodness-of-fit and for assessing the significance of model covariates.

Modelling the influence of biotic factors on species distribution patterns

Biotic interactions can have large effects on species distributions yet their role in shaping species ranges is seldom explored due to historical difficulties in incorporating biotic factors into models without a priori knowledge on interspecific interactions. Improved SDMs, which account for biotic factors and do not require a priori knowledge on species interactions, are needed to fully understand species distributions. Here, we model the influence of abiotic and biotic factors on species distribution patterns and explore the robustness of distributions under future climate change. We fit hierarchical spatial models using Integrated Nested Laplace Approximation (INLA) for lagomorph species throughout Europe and test the predictive ability of models containing only abiotic factors against models containing abiotic and biotic factors. We account for residual spatial autocorrelation using a conditional autoregressive (CAR) model. Model outputs are used to estimate areas in which abiotic and biotic factors determine species’ ranges. INLA models containing both abiotic and biotic factors had substantially better predictive ability than models containing abiotic factors only, for all but one of the four species. In models containing abiotic and biotic factors, both appeared equally important as determinants of lagomorph ranges, but the influences were spatially heterogeneous. Parts of widespread lagomorph ranges highly influenced by biotic factors will be less robust to future changes in climate, whereas parts of more localised species ranges highly influenced by the environment may be less robust to future climate. SDMs that do not explicitly include biotic factors are potentially misleading and omit a very important source of variation. For the field of species distribution modelling to advance, biotic factors must be taken into account in order to improve the reliability of predicting species distribution patterns both presently and under future climate change.

Behavioural context of multi-scale species distribution models assessed by radio-tracking

Incorporating ecological processes and animal behaviour into Species Distribution Models (SDMs) is difficult. In species with a central resting or breeding place, there can be conflict between the environmental requirements of the 'central place' and foraging habitat. We apply a multi-scale SDM to examine habitat trade-offs between the central place, roost sites, and foraging habitat in . Myotis nattereri. We validate these derived associations using habitat selection from behavioural observations of radio-tracked bats. A Generalised Linear Model (GLM) of roost occurrence using land cover variables with mixed spatial scales indicated roost occurrence was positively associated with woodland on a fine scale and pasture on a broad scale. Habitat selection of radio-tracked bats mirrored the SDM with bats selecting for woodland in the immediate vicinity of individual roosts but avoiding this habitat in foraging areas, whilst pasture was significantly positively selected for in foraging areas. Using habitat selection derived from radio-tracking enables a multi-scale SDM to be interpreted in a behavioural context. We suggest that the multi-scale SDM of . M. nattereri describes a trade-off between the central place and foraging habitat. Multi-scale methods provide a greater understanding of the ecological processes which determine where species occur and allow integration of behavioural processes into SDMs. The findings have implications when assessing the resource use of a species at a single point in time. Doing so could lead to misinterpretation of habitat requirements as these can change within a short time period depending on specific behaviour, particularly if detectability changes depending on behaviour. © 2011 Gesellschaft für ökologie.

Species distribution and coordination of uranyl chloro complexes in acetonitrile

The complex formation of the uranyl ion, UO22+, with chloride ions in acetonitrile has been investigated by factor analysis of UV-vis absorption and U L-3 edge EXAFS (extended X-ray absorption fine structure) spectra. As a function of increasing [Cl-]/[UO22+] ratio, the five monomeric species [UO2(H2O)(5)](2+), [UO2Cl(H2O)(2)(MeCN)(2)](+), [UO2Cl2(H2O)(MeCN)(2)], [UO2Cl3(MeCN)(2)](-), and [UO2Cl4](2-) have been observed. The distances determined in the first coordination sphere are: U-O-ax = 1.77 angstrom, U-O-H2O = 2.43 angstrom, U-N-MeCN = 2.53 angstrom, and U-Cl = 2.68 angstrom. A crystalline material has been obtained from the intermediate solution with the [Cl-]/[UO22+] ratio of similar to 2, where [UO2Cl2(H2O)(MeCN)(2)] is the dominating species. The crystal structure analysis of this material revealed a tetrameric complex, [(UO2)(4)(mu(2)-Cl)(4)(mu(3)-O)(2)(H2O)(2)(CH3CN)(4)]center dot(CH3CN). The crystal data are: monoclinic, space group P2(1)/n, a 10.6388(5) angstrom, b = 14.8441(5) angstrom, c = 10.8521(5) angstrom, beta = 109.164(5)degrees, and Z = 2. The U(VI) coordination of the solution species [UO2Cl2(H2O)(MeCN)(2)] changes during the crystallization by replacing one MeCN molecule with a bridging mu(3)-O atom in the tetramer.

The effects of past, present and future climate change on range-wide genetic diversity in northern North Atlantic marine species

It is now accepted that changes in the Earth’s climate are having a profound effect on the distributions of a wide variety of species. One aspect of these changes that has only recently received any attention, however, is their potential effect on levels of within-species genetic diversity. Theoretical, empirical and modelling studies suggest that the impact of trailing-edge population extirpation on range-wide intraspecific diversity will be most pronounced in species that harbour the majority of their genetic variation at low latitudes as a result of changes during the Quaternary glaciations. In the present review, I describe the historical factors that have determined current patterns of genetic variation across the ranges of Northern North Atlantic species, highlight the fact that the majority of these species do indeed harbour a disproportionate level of genetic diversity in rear-edge populations, and outline how combined species distribution modelling and genetic analyses can provide insights into the potential effects of climate change on their overall genetic diversity.

Proteomics on porcine haptoglobin and IgG/IgA show protein species distribution and glycosylation pattern to remain similar in PCV2-SD infection

Haptoglobin (Hp) and immunoglobulins are plasma glycoproteins involved in the immune reaction of the organism after infection and/or inflammation. Porcine circovirus type 2-systemic disease (PCV2-SD), formerly known as postweaning multisystemic wasting syndrome (PMWS), is a globally spread pig disease of great economic impact. PCV2-SD affects the immunological system of pigs causing immunosuppression. The aim of this work was to characterize the Hp protein species of healthy and PCV2-SD affected pigs, as well as the protein backbone and the glycan chain composition of porcine Hp. PCV2-SD affected pigs had an increased overall Hp level, but it did not affect the ratio between Hp species. Glycoproteomic analysis of the Hp β subunits confirmed that porcine Hp is N-glycosylated and, unexpectedly, O-glycosylated, a PTM that is not found on Hp from healthy humans. The glyco-profile of porcine IgG and IgA heavy chains was also characterized; decreased levels of both proteins were found in the investigated group of PCV2-SD affected pigs. Obtained results indicate that no significant changes in the N- and O-glycosylation patterns of these major porcine plasma glycoproteins were detectable between healthy and PCV2-SD affected animals.

Biogeography, macroecology and species’ traits mediate competitive interactions in the order Lagomorpha

1. In addition to abiotic determinants, biotic factors, including competitive, interspecific interactions, limit species’ distributions. Environmental changes in human disturbance, land use and climate are predicted to have widespread impacts on interactions between species, especially in the order Lagomorpha due to the higher latitudes and more extreme environmental conditions they occupy.
2. We reviewed the published literature on interspecific interactions in the order Lagomorpha, and compared the biogeography, macroecology, phylogeny and traits of species known to interact with those of species with no reported interactions, to investigate how projected future environmental change may affect interactions and potentially alter species’ distributions.
3. Thirty-three lagomorph species have competitive interactions reported in the literature; the majority involve hares (Lepus sp.) or the eastern cottontail rabbit (Sylvilagus floridanus). Key regions for interactions are located between 30-50°N of the Equator, and include eastern Asia (southern Russia on the border of Mongolia) and North America (north western USA).
4. Closely related, large-bodied, similarly sized species occurring in regions of human-modified, typically agricultural landscapes, or at high elevations are significantly more likely to have reported competitive interactions than other lagomorph species.
5. We identify species’ traits associated with competitive interactions, and highlight some potential impacts that future environmental change may have on interspecific interactions. Our approach using bibliometric and biological data is widely applicable, and with relatively straightforward methodologies, can provide insights into interactions between species.
6. Our results have implications for predicting species’ responses to global change, and we advise that capturing, parameterizing and incorporating interspecific interactions into analyses (for example, species distribution modelling) may be more important than suggested by the literature.

A new statistical framework for the quantification of covariate associations with species distributions

Identifying processes that shape species geographical ranges is a prerequisite for understanding environmental change. Currently, species distribution modelling methods do not offer credible statistical tests of the relative influence of climate factors and typically ignore other processes (e.g. biotic interactions and dispersal limitation). We use a hierarchical model fitted with Markov Chain Monte Carlo to combine ecologically plausible niche structures using regression splines to describe unimodal but potentially skewed response terms. We apply spatially explicit error terms that account for (and may help identify) missing variables. Using three example distributions of European bird species, we map model results to show sensitivity to change in each covariate. We show that the overall strength of climatic association differs between species and that each species has considerable spatial variation in both the strength of the climatic association and the sensitivity to climate change. Our methods are widely applicable to many species distribution modelling problems and enable accurate assessment of the statistical importance of biotic and abiotic influences on distributions.

Coherence and discontinuity in the scaling of species' distribution patterns

The spatial distribution of a species can be characterized at many different spatial scales, from fine-scale measures of local population density to coarse-scale geographical-range structure. Previous studies have shown a degree of correlation in species' distribution patterns across narrow ranges of scales, making it possible to predict fine-scale properties from coarser-scale distributions. To test the limits of such extrapolation, we have compiled distributional information on 16 species of British plants, at scales ranging across six orders of magnitude in linear resolution (1 in to 100 km). As expected, the correlation between patterns at different spatial scales tends to degrade as the scales become more widely separated. There is, however, an abrupt breakdown in cross-scale correlations across intermediate (ca. 0.5 km) scales, suggesting that local and regional patterns are influenced by essentially non-overlapping sets of processes. The scaling discontinuity may also reflect characteristic scales of human land use in Britain, suggesting a novel method for analysing the 'footprint' of humanity on a landscape.

Restrospective genetic monitoring of the threatened Yellow marsh saxifrage (Saxifraga hirculus) reveals genetic erosion but provides valuable information for conservation strategies

Aim: Retrospective genetic monitoring, comparing genetic diversity of extant populations with historical samples, can provide valuable and often unique insights into evolutionary processes informing conservation strategies. The Yellow marsh saxifrage (Saxifraga hirculus) is listed as ‘critically endangered’ in Ireland with only two extant populations. We quantified genetic changes over time and identified genotypes in extant populations that could be used as founders for reintroductions to sites where the species is extinct.

Location: Ireland.

Methods: Samples were obtained from both locations where the species is currently found, including the most threatened site at the Garron Plateau, Co. Antrim, which held only 13 individuals during 2011. Herbarium samples covering the period from 1886 to 1957 were obtained including plants from the same area as the most threatened population, as well as three extinct populations. In total, 422 individuals (319 present-day and 103 historical) were genotyped at six microsatellite loci. Species distribution modelling was used to identify areas of potentially suitable habitat for reintroductions.

Results: Level of phenotypic diversity within the most threatened population was significantly lower in the present-day compared with historical samples but levels of observed heterozygosity and number of alleles, whilst reduced, did not differ significantly. However, Bayesian clustering analysis suggested gradual lineage replacement over time. All three measures of genetic diversity were generally lower at the most threatened population compared with the more substantial extant populations in Co. Mayo. Species distribution modelling suggested that habitat at one site where the species is extinct may be suitable for reintroduction.

Main conclusions: The dominant genetic lineage in the most threatened population is rare elsewhere; thus, care needs to be taken when formulating any potential reintroduction programme. Our findings highlight both the need for genetic monitoring of threatened populations, but also for its swift implementation before levels of diversity become critically low.

Cryptic introgression into the Kidney saxifrage (Saxifraga hirsuta) from its more abundant sympatric congener Saxifraga spathularis, and the potential risk of genetic assimilation

Background and Aims: Although hybridization can play a positive role in plant evolution, it has been shown that excessive unidirectional hybridization can result in replacement of a species’ gene pool, and even the extinction ofrare species via genetic assimilation. This study examines levels of introgression between the common Saxifraga spathularis and its rarer congener S. hirsuta, which have been observed to hybridize in the wild where they occursympatrically. 
Methods: Seven species-specific single nucleotide polymorphisms (SNPs) were analysed in 1025 plants representing both species and their hybrid, S. polita, from 29 sites across their ranges in Ireland. In addition, species distributionmodelling was carried out to determine whether the relative abundance of the two parental species is likely to change under future climate scenarios. 
Key Results: Saxifraga spathularis individuals tended to be genetically pure, exhibiting little or no introgression from S. hirsuta, but significant levels of introgression of S. spathularis alleles into S. hirsuta were observed, indicatingthat populations exhibiting S. hirsuta morphology are more like a hybrid swarm, consisting of backcrosses and F2s. Populations of the hybrid, S. polita, were generally comprised of F1s or F2s, with some evidence of backcrossing. Species distribution modelling under projected future climate scenarios indicated an increase in suitable habitats for both parental species.
Conclusions: Levels of introgression observed in this study in both S. spathularis and S. hirsuta would appear to be correlated with the relative abundance of the species. Significant introgression of S. spathularis alleles was detectedin the majority of the S. hirsuta populations analysed and, consequently, ongoing introgression would appear to represent a threat to the genetic integrity of S. hirsuta, particularly in areas where the species exists sympatricallywith its congener and where it is greatly outnumbered.

New insights on postglacial colonization in western Europe: the phylogeography of the Leisler’s bat (Nyctalus leisleri)

Despite recent advances in the understanding of the interplay between a dynamic physical environment and phylogeography in Europe, the origins of contemporary Irish biota remain uncertain. Current thinking is that Ireland was colonized post-glacially from southern European refugia, following the end of the last glacial maximum(LGM), some 20 000 years BP. The Leisler’s bat (Nyctalus leisleri), one of the few native Irish mammal species, is widely distributed throughout Europe but, with the exception of Ireland, is generally rare and considered vulnerable. We investigate the origins and phylogeographic relationships of Irish populations in relation to those across Europe, including the closely related species N. azoreum. We use a combination of approaches, including mitochondrial and nuclear DNA markers, in addition to approximate Bayesian computation and palaeo-climatic species distribution modelling. Molecular analyses revealed two distinct and diverse European mitochondrialDNAlineages,which probably diverged in separate glacial refugia. Awestern lineage, restricted to Ireland, Britain and the Azores, comprises Irish and British N. leisleri and N. azoreum specimens; an eastern lineage is distributed throughout mainland Europe. Palaeo-climatic projections indicate suitable habitats during the LGM, including known glacial refugia, in addition to potential novel cryptic refugia along the western fringe of Europe. These results may be applicable to populations of many species.

Large-scale spatial patterns in the distribution of Collembola (Hexapoda) species in Antarctic terrestrial ecosystems

We tested whether the distribution of three common springtail species (Gressittacantha terranova, Gomphiocephalus hodgsoni and Friesea grisea) in Victoria Land (Antarctica) could be modelled as a function of latitude, longitude, altitude and distance from the sea.

Victoria Land, Ross Dependency, Antarctica.

Generalized linear models were constructed using species presence/absence data relative to geographical features (latitude, longitude, altitude, distance from sea) across the species' entire ranges. Model results were then integrated with the known phylogeography of each species and hypotheses were generated on the role of climate as a major driver of Antarctic springtail distribution.

Based on model selection using Akaike's information criterion, the species' distributions were: hump-shaped relative to longitude and monotonic with altitude for Gressittacantha terranova; hump-shaped relative to latitude and monotonic with altitude for Gomphiocephalus hodgsoni; and hump-shaped relative to longitude and monotonic with latitude, altitude and distance from the sea for Friesea grisea.

No single distributional pattern was shared by the three species. While distributions were partially a response to climatic spatial clines, the patterns observed strongly suggest that past geological events have influenced the observed distributions. Accordingly, present-day spatial patterns are likely to have arisen from the interaction of historical and environmental drivers. Future studies will need to integrate a range of spatial and temporal scales to further quantify their respective roles.