Niche overlap and species co-occurrence patterns in carabid communities of the northern Chinese steppes

Understanding how species sort themselves into communities is essential to explain the mechanisms that maintain biodiversity. Important insights into potential mechanisms of coexistence may be obtained from observation of non-random patterns in community assembly. The spatial niche overlap (Pianka index) and co-occurrence (c-score) patterns in carabid species in three types of steppes (desert steppe, typical steppe, and meadow steppe) in China was investigated. Non randomness was tested using null models. Niche overlap values were significantly higher than expected by chance in the desert steppe, where vegetation cover is less abundant and less uniformly distributed, which possibly forces species to concentrate in certain places. In the typical and meadow steppes, results were influenced by the scale of the analysis. At a broad scale, niche separation was found as a result of species segregation among different sectors (habitats) within these steppes, but when the analysis was conducted at a finer scale, species appeared to be no more segregated than expected by chance. The high co-occurrence averages found in the meadow and typical steppes indicate that the distributions of the species found in a site may be negatively affected by the presence of other species, which suggests that some species tend to exclude (or reduce the abundance of) others. The very low c-score average observed in the desert steppe suggests that competition is not involved there. Thus, in more homogeneous landscapes (such as the typical and meadow steppes), competition might play some role in community structure, whereas spatial variation in the abundances of species is more driven by the uneven spatial distribution of vegetation in the landscape where productivity is lower and less uniformly distributed.

Biophony in a noisy tropical urban forest fragment

Anthropogenic noise, which is part of an urban soundscape, can negatively affect the behaviour of wild animals. Here we investigated how biophony (animal sounds) was affected by noise in an urban Brazilian forest fragment. Our hypothesis was that noise and biophony would differ between the border and the centre of the forest fragment (i.e., lower biophony predicted in noisy areas). Two passive acoustic monitoring devices were used to record soundscapes one week per month, 24 hour per day, from May to July 2012. The Acoustic Complexity Index (ACI) was used to quantify biophony and the Power Spectral Density (PSD) to quantify urban noise. PSD and ACI were higher on the border than in the centre of the fragment. PSD was lower in July, while the ACI did not significantly vary between months. Noise levels were also higher on the border. Conversely, potential species richness was higher in the centre of the forest fragment. Higher biophony at noisy sites can be interpreted as behavioural responses of species for communicating in noisy areas. Alternatively, they could be the result of species segregation by degree of vocal plasticity or due to differences in composition of communities.

Varying richness need not imply non-random species co-occurrence: implications for specifying null models

BackgroundNon-random species co-occurrence is of fundamental interest to ecologists. One approach to analysing non-random patterns is null modelling. This involves calculation of a metric for the observed dataset, and comparison to a distribution obtained by repeatedly randomising the data. Choice of randomisation algorithm, specifically whether null model species richness is fixed at that of the observed dataset, is likely to affect model results. This is particularly important in cases when there is high variation in species richness between sampling units in the observed data.MethodsHere I demonstrate the effects of accounting for variation in species richness. I use the C-score, a metric measuring species segregation as “checkerboard units”, applied to 289 datasets. First, I run null models in which sites are equally likely to be occupied (fixed-equiprobable algorithm). I do this both for the original datasets, and for the same datasets where occurrences are randomised with the species richness distribution fixed (pre-randomised datasets). Second, I run null models that fix site species richness to that observed (fixed-fixed algorithm).ResultsFor real datasets, using the fixed-equiprobable algorithm (sites are equally likely to be colonised), C-score standardised effect size (SES) was positively related to variability in species richness between sites within a dataset. This effect was also found for pre-randomised datasets, indicating that variability in species richness can be exclusively responsible for detection of non-random species co-occurrence. When using the fixed-fixed algorithm (richness is constrained to that of real sites), there was no relationship between SES and variability in species richness. There was also a reverse in the effect direction, with 94% of significant tests indicating a lower C-score than expected for the fixed-equiprobable algorithm, but 98% of significant tests indicating a higher C-score than expected for the fixed-fixed algorithm.DiscussionI speculate that when variation in species richness is high, fewer checkerboard units are possible, regardless of segregation between species. Therefore, use of fixed-equiprobable algorithms in situations where real species richness is highly variable between sites within a dataset will yield significant results, even if species co-occur randomly within the constraints of the species richness distribution. Consequently, use of such tests makes the a priori assumption that high within-dataset variation in species richness indicates non-random species co-occurrence. I recommend using algorithms that explicitly take into account species richness distributions when one wants to eliminate the effect of richness variation in terms of producing significant but spurious positive co-occurrence results. Alternatively, non-null mechanistic models can be created, in which hypothesised species assembly processes must be explicitly stated and tested.

Detection of Recombinant Hare Myxoma Virus in Wild Rabbits (Oryctolagus cuniculus algirus)

In late 2018, an epidemic myxomatosis outbreak emerged on the Iberian Peninsula leading to high mortality in Iberian hare populations. A recombinant Myxoma virus (strains MYXV-Tol and ha-MYXV) was rapidly identified, harbouring a 2.8 kbp insertion containing evolved duplicates of M060L, M061L, M064L, and M065L genes from myxoma virus (MYXV) or other Poxviruses. Since 2017, 1616 rabbits and 125 hares were tested by a qPCR directed to M000.5L/R gene, conserved in MYXV and MYXV-Tol/ha-MYXV strains. A subset of the positive samples (20%) from both species was tested for the insert with MYXV being detected in rabbits and the recombinant MYXV in hares. Recently, three wild rabbits were found dead South of mainland Portugal, showing skin oedema and pulmonary lesions that tested positive for the 2.8 kbp insert. Sequencing analysis showed 100% similarity with the insert sequences described in Iberian hares from Spain. Viral particles were observed in the lungs and eyelids of rabbits by electron microscopy, and isolation in RK13 cells attested virus infectivity. Despite that the analysis of complete genomes may predict the recombinant MYXV strains’ ability to infect rabbit, routine analyses showed species segregation for the circulation of MYXV and recombinant MYXV in wild rabbit and in Iberian hares, respectively. This study demonstrates, however, that recombinant MYXV can effectively infect and cause myxomatosis in wild rabbits and domestic rabbits, raising serious concerns for the future of the Iberian wild leporids while emphasises the need for the continuous monitoring of MYXV and recombinant MYXV in both species.

Detection of Recombinant Hare Myxoma Virus in Wild Rabbits (Oryctolagus cuniculus algirus)

In late 2018, an epidemic myxomatosis outbreak emerged on the Iberian Peninsula leading to high mortality in Iberian hare populations. Soon, a recombinant virus (MYXV-Tol or ha-MYXV) was identified, harboring a 2.8 kb insertion containing evolved duplicates of M060L, M061L, M064L, and M065L from MYXV. Since 2017, 1616 rabbits and 82 hares were tested by a qPCR directed to M000.5L/R gene, conserved in MYXV and MYXV-Tol/ ha-MYXV strains. A subset (20%) of the positive samples was tested for the insert with MYXV being detected in rabbits and recombinant MYXV in hares. Recently, two wild rabbits found dead in South Portugal, showing skin oedema and pulmonary lesions tested positive for the 2.8 Kb insert. Sequencing showed 100% similarity with the insert sequences described in Iberian hares from Spain. Viral particles were observed in the lungs of both rabbits by electron microscopy, and isolation in RK13 cells showed virus infectivity. Despite the analysis of recombinant MYXV genomes may predict its ability to infect rabbit, routine analyses showed species segregation for the circulation of MYXV and recombinant MYXV in wild rabbit and in Iberian hares, respectively. This study demonstrates, however, that recombinant MYXV can effectively infect and cause myxomatosis in wild rabbits and domestic rabbits, which raises serious concerns for the future of the Iberian wild leporids and emphasizes the need to continue monitoring MYXV and recombinant MYXV in both species.

Leaf Habit and Stem Hydraulic Traits Determine Functional Segregation of Multiple Oak Species along a Water Availability Gradient

Oaks are a dominant woody plant genus in the northern hemisphere that occupy a wide range of habitats and are ecologically diverse. We implemented a functional trait approach that included nine functional traits related to leaves and stems in order to explain the species coexistence of 21 oak species along a water availability gradient in a temperate forest in Mexico. This particular forest is characterized as a biodiversity hotspot, with many oak species including some endemics. Our main aim was to investigate whether the different oak species had specific trait associations that allow them to coexist along an environmental gradient at regional scale. First, we explored trait covariation and determined the main functional dimensions in which oaks were segregated. Second, we explored how environmental variation has selected for restricted functional dimensions that shape oak distributions along the gradient, regardless of their leaf life span or phylogeny (section level). Third, we quantified the niche overlap between the oak functional spaces at different levels. The analyzed species showed three functional dimensions of trait variation: a primary axis related to the leaf economic spectrum, which corresponds to the segregation of the species according to leaf habit; a second axis that reflects the stem hydraulic properties and corresponds to species segregation followed by phylogenetic segregation, reflecting some degree of trait conservatism, and a third axis, represented mainly by leaf area and plant height, that corresponds to species segregation. Finally, our findings indicated that the functional space measured with leaf traits and stem traits such as hydraulic capacity was integrally linked to niche differentiation. This linkage suggests that the earliest mechanism of species segregation was related to habitat suitability and that the stem hydraulic trade-off reflects differences between phylogenetic sections; these traits may promote coexistence between distantly related oak species.

On the steady-states of a two-species non-local cross-diffusion model

We investigate the existence and properties of steady-state solutions to a degenerate, non-local system of partial differential equations that describe two-species segregation in homogeneous and heterogeneous environments. This is accomplished via the analysis of the existence and non-existence of global minimizers to the corresponding free energy functional. We prove that in the spatially homogeneous case global minimizers exist if and only if the mass of the potential governing the intra-species attraction is sufficiently large and the support of the potential governing the interspecies repulsion is bounded. Moreover, when they exist they are such that the two species have disjoint support, leading to complete segregation. For the heterogeneous environment we show that if a sub-additivity condition is satisfied then global minimizers exists. We provide an example of an environment that leads to the sub-additivity condition being satisfied. Finally, we explore the bounded domain case with periodic conditions through the use of numerical simulations.

Sex aggregation and species segregation cues in swarming mosquitoes: role of ground visual markers

Background Mating swarm segregation in closely related insect species may contribute to reproductive isolation. Visual markers are used for swarm formation; however, it is unknown whether they play a key role in swarm location, species segregation and sex aggregation. Methods Using two sympatric closely related species of the Anopheles gambiae complex, An. coluzzii and An. gambiae (s.s.), we investigated in both laboratory and semi-field conditions (i) whether males of the two species use visual markers (black cloths) to locate their swarm; and (ii) whether the presence/absence and size of the marker may differentially affect swarm characteristics. We also investigated whether conspecific virgin females use these markers to join male swarm sites. Results We showed that males of the two species used visual markers but in different ways: An. coluzzii swarm right above the marker whereas An. gambiae (s.s.) locate their swarm at a constant distance of 76.4 ± 0.6 cm from a 20 × 20 cm marker in the laboratory setup and at 206 ± 6 cm from a 60 × 60 cm marker in the semi-field setup. Although increased marker size recruited more mosquitoes and consequently increased the swarm size in the two species, An. coluzzii swarms flew higher and were stretched both vertically and horizontally, while An. gambiae (s.s.) swarms were only stretched horizontally. Virgin females displayed a swarm-like behavior with similar characteristics to their conspecific males. Conclusions Our results provided experimental evidence that both An. coluzzii and An. gambiae (s.s.) males use ground visual markers to form and locate their swarm at species-specific locations. Moreover, the marker size differentially affected swarm characteristics in the two species. Our results also showed that virgin females displayed a swarm-like behavior. However, these “swarms” could be due to the absence of males in our experimental conditions. Nevertheless, the fact that females displayed these “swarms” with the same characteristics as their respective males provided evidence that visual markers are used by the two sexes to join mating spots. Altogether, this suggests that visual markers and the way species and sexes use them could be key cues in species segregation, swarm location and recognition.