Ecological thresholds: an assessment of methods to identify abrupt changes in species–habitat relationships

Habitat thresholds are usually defined as “points of abrupt change” in the species–habitat relationships. Habitat thresholds can be a key tool for understanding species requirements, and provide an objective definition of conservation targets, by identifying when habitat loss leads to a rapid loss of species, and the minimum amount of habitat necessary for species persistence. However, a large variety of statistical methods have been used to analyse them. In this context, we reviewed these methods and, using simulated data sets, we tested the main models to compare their performance on the identification of thresholds. We show that researchers use very different analytical tools, corresponding to different operational definitions of habitat thresholds, which can considerably affect their detection. Piecewise regression and generalized additive models allow both the distinction between linear and nonlinear dynamics, and the correct identification of break point position. In contrast, other methods such as logistic regression fail because they may incorrectly detect thresholds in gradual patterns, or they may over or underestimate the threshold position. In conservation or habitat modelling, it is important to focus efforts efficiently and the inappropriate choice of statistical methods may have detrimental consequences.     

Combining genetic and ecological data to assess the conservation status of the endangered Ethiopian walia ibex

Knowledge about the phylogenetic history, genetic variation and ecological requirements of a species is important for its conservation and management. Unfortunately, for many species this information is lacking. Here we use multiple approaches (phylogenetics, population genetics and ecological modelling) to evaluate the evolutionary history and conservation status of Capra walie , an endangered flagship species of wild goat endemic to Ethiopia. The analysis of mitochondrial cytochrome b and Y-chromosome DNA sequences suggests that C. walie forms a monophyletic clade with Capra nubiana , but potentially has been isolated for up to 0.8 million years from this closely related species. Microsatellite DNA analyses show that C. walie has very low genetic variation (mean heterozygosity=0.35) compared with other endangered mammals. This reduced variation likely derives from a prolonged demographic decline and small effective population size. Ecological niche modelling using the bioclimatic features of habitats occupied by C. walie , suggests ecological differences between C. walie and C. nubiana , and identifies the areas most suitable for future reintroductions of C. walie . The genetic and bioclimatic data suggest that C. walie is distinct and requires immediate conservation actions including genetic monitoring and reintroductions to establish independent populations. This study illustrates how combining noninvasive sampling along with genetic and ecological (bioclimatic) approaches can help assess conservation status of poorly known species.     

Ecogeographical variation of body size in the newt Triturus carnifex: comparing the hypotheses using an information‐theoretic approach

Aim Ecogeographical variation of body size in vertebrates (e.g. Bergmann's rule) has long been recognized. However, the patterns and causes of intra‐specific ecogeographical variation of body size in ectotherms, and in amphibians in particular, are strongly debated. We identified the relationship between bioclimatic variables and body size predicted a priori by alternative hypotheses (heat balance, endurance, seasonality, starvation resistance, water availability, primary productivity, parental investment) proposed to explain ecogeographical patterns of body size in ectotherms, and we evaluated the relative support of these hypotheses in explaining variation in body size of the Italian crested newt, Triturus carnifex. Location Twenty‐three populations covering the whole range of T. carnifex (Austria, Croatia, Italy and Slovenia). Methods We obtained data on body size (snout–vent length, SVL) of 2639 adult newts from direct measurements and the literature; we obtained high‐resolution environmental data for the sampled localities. We used an information‐theoretic approach to evaluate the support of the data for the different hypotheses. We also integrated information on population genetics in our models. Results We observed strong geographical variation of body size. The best Akaike information criterion (AIC) models showed that populations with larger body size are associated with cold climates and secondarily with high primary productivity. Furthermore, sexual dimorphism increases in cold climates, as the increase in body size was stronger for females. When taking into account population genetics, we did not find support for relationships with the other variables. Main conclusion Our results are consistent with three hypotheses proposed to explain ecogeographical variation in amphibians: heat balance, increased parental investment of females and productivity. Information theory provides the framework for comparing hypotheses rather than looking for patterns. We suggest that evaluating the support for mechanisms can provide better insights than simply assessing whether ecogeographical variation is in agreement with some ‘rule’.     

Patterns of diversity in microscopic animals: are they comparable to those in protists or in larger animals?

Aim General patterns of biodiversity, such as latitudinal gradients and species‐area relationships, are found consistently in a wide range of organisms, but recent results for protist diversity suggest that organisms shorter than 2 mm do not display such patterns. We tested this prediction in bdelloid rotifers, pluricellular metazoans smaller than 2 mm, but with size and ecology comparable to protists. Location A single valley in northern Italy was surveyed in detail and compared to all available faunistic data on bdelloids worldwide. Methods We analysed 171 local assemblages of bdelloid rotifers living in 5 systems of dry mosses and submerged mosses in running water and in lakes. We compared patterns of alpha, beta, and gamma diversity, and nestedness of metacommunities, with those known from protists and larger organisms. Results Bdelloid rotifers showed low local species richness (alpha diversity), with strong habitat selection, as observed in larger organisms. The number of species differed among systems, with a higher number of species in dry than in aquatic mosses. There was no hierarchical structure or exclusion of species in the metacommunity pattern within each system. Local diversity for the entire valley was surprisingly high compared with worldwide bdelloid diversity, similar to observed patterns in protists. Main Conclusions Bdelloid rotifers have some of the peculiarities of protist biodiversity, although at slightly different spatial scales, thus confirming the idea of a major change in biodiversity patterns among organisms shorter than 2 mm. However, bdelloids show stronger habitat selection than protists. We suggest two possible explanations for the observed patterns: (1) dispersal is very rare, and not all bdelloid clones are arriving everywhere; and (2) dispersal is effective in displacing propagules, but environmental heterogeneity is very high and prevents many species from colonizing a given patch of moss.     

BH3‐in‐groove dimerization initiates and helix 9 dimerization expands Bax pore assembly in membranes

Pro‐apoptotic Bax induces mitochondrial outer membrane permeabilization (MOMP) by forming oligomers through a largely undefined process. Using site‐specific disulfide crosslinking, compartment‐specific chemical labeling, and mutational analysis, we found that activated integral membrane Bax proteins form a BH3‐in‐groove dimer interface on the MOM surface similar to that observed in crystals. However, after the α5 helix was released into the MOM, the remaining interface with α2, α3, and α4 helices was rearranged. Another dimer interface was formed inside the MOM by two intersected or parallel α9 helices. Combinations of these interfaces generated oligomers in the MOM. Oligomerization was initiated by BH3‐in‐groove dimerization, without which neither the other dimerizations nor MOMP occurred. In contrast, α9 dimerization occurred downstream and was required for release of large but not small proteins from mitochondria. Moreover, the release of large proteins was facilitated by α9 insertion into the MOM and localization to the pore rim. Therefore, the BH3‐in‐groove dimerization on the MOM nucleates the assembly of an oligomeric Bax pore that is enlarged by α9 dimerization at the rim.     

TetraDENSITY: A database of population density estimates in terrestrial vertebrates

Motivation

Population density is a key demographic parameter influencing many ecological processes, and macroecology has described both intra‐ and interspecific patterns of variation. Population density data are expensive to collect and contain many forms of noise and potential bias; these factors have impeded investigation of macroecological patterns, and many hypotheses remain largely unexplored. Population density also represents fundamental information for conservation, because it underlies population dynamics and, ultimately, extinction risk. Here we present TetraDENSITY, an extensive dataset with > 18,000 records of density estimates for terrestrial vertebrates, in order to facilitate new research on this topic.

Main types of variable contained

The dataset includes taxonomic information on species, population density estimate, year of data collection, season, coordinates of the locality, locality name, habitat, sampling method and sampling area.

Spatial location and grain

Global. Spatial accuracy varies across studies; conservatively, it can be considered at 1°, but for many data it is much finer.

Time period and grain

From 1926 to 2017. Temporal accuracy is yearly in most cases, but studies with higher temporal resolution (season, month) are also present.

Major taxa and level of measurement

Amphibians in terrestrial phase, reptiles, birds and mammals. Estimates derive from multiple methods, reflecting the study taxon, location and techniques available at the time of density estimation.     

Causes and consequences of crayfish extinction: Stream connectivity,habitat changes,alien species and ecosystem services

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Genetic and ecological data reveal species boundaries between viviparous and oviparous lizard lineages

Identification of cryptic species is an essential aim for conservation biologists to avoid premature extinctions of ‘unrecognized'' species. Integrating different types of data can undoubtedly aid in resolving the issue of species delimitation. We studied here two lineages of the common lizard Zootoca vivipara that display different reproductive mode (the viviparous Z. v. vivipara and the oviparous Z. v. carniolica) and that overlap their distributional ranges in the European Alps. With the purpose of delimiting species'' boundaries, we analyzed their ecological, genetic and natural history features. More than 300 samples were collected and analyzed at cytochrome b and 11 microsatellites loci for investigating genetic variation, population structure, individual relatedness and evolutionary histories of the two lineages. Additionally, we compared their ecological niches using eight ecological variables. Genetic data showed contrasting patterns of genetic structure between the two lineages, different demographic dynamics and no hybridization events. Also strong ecological differences (such as temperature) emerged between the two lineages, and niche overlap was limited. Taken together, these results indicate that Z. v. vivipara and Z. v. carniolica should be recognized as two separate species, and particular conservation consideration should be given to the oviparous lineage that tends to live in areas threatened by increasing impact of human activities. However, recent and rapid climate warming might determine an increasing risk for the persistence of the viviparous lineage, being adapted to cold environments.     

Biphasic predators provide biomass subsidies in small freshwater habitats: A case study of spring and cave pools

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